diff --git a/andv/NC_003466.1.fasta b/andv/NC_003466.1.fasta deleted file mode 100644 index bc89f0b..0000000 --- a/andv/NC_003466.1.fasta +++ /dev/null @@ -1 +0,0 @@ -TAGTAGTAGACTCCTTGAGAAGCTACTGCTGCGAAAGCTGGAATGAGCACCCTCCAAGAATTGCAGGAAAACATCACAGCACACGAACAACAGCTCGTGACTGCTCGGCAAAAGCTTAAGGATGCCGAGAAGGCAGTGGAGGTGGACCCGGATGACGTTAACAAGAGCACACTACAAAGTAGACGGGCAGCTGTGTCTACATTGGAGACCAAACTCGGAGAACTTAAGAGGCAACTTGCAGATTTGGTGGCAGCTCAAAAATTGGCTACAAAACCAGTTGATCCAACAGGGCTTGAGCCTGATGATCATCTAAAGGAAAAATCATCTCTGAGATATGGGAATGTCCTGGATGTTAATTCAATTGATTTGGAAGAACCGAGTGGACAGACTGCTGATTGGAAGGCTATAGGAGCATACATCTTAGGGTTTGCAATTCCGATCATCCTAAAGGCCTTATACATGCTGTCAACCCGTGGGAGACAAACTGTGAAAGACAACAAAGGGACCAGGATAAGGTTTAAGGATGATTCTTCCTTTGAAGAAGTCAATGGGATACGTAAACCAAAACACCTTTACGTCTCAATGCCAACTGCACAGTCCACTATGAAGGCTGAAGAAATCACGCCAGGACGATTTAGGACAATTGCTTGTGGCCTTTTTCCAGCACAGGTCAAAGCCCGAAATATAATAAGTCCTGTAATGGGAGTAATTGGATTTGGCTTCTTTGTAAAGGATTGGATGGATCGGATAGAAGAGTTTCTGGCTGCAGAGTGTCCATTCTTACCTAAGCCAAAGGTCGCCTCAGAAGCCTTCATGTCTACCAATAAGATGTATTTTCTGAACAGACAGAGACAAGTCAATGAATCTAAGGTTCAAGATATTATCGATTTGATAGACCATGCTGAGACCGAGTCTGCTACCTTGTTTACAGAGATTGCAACACCCCATTCAGTCTGGGTGTTTGCATGTGCACCTGACCGGTGCCCTCCAACTGCATTGTATGTTGCAGGGGTACCGGAACTTGGTGCATTTTTTTCTATCCTTCAGGACATGCGTAATACCATCATGGCATCTAAATCTGTAGGGACTGCAGAAGAGAAGCTAAAGAAAAAATCTGCCTTCTACCAATCATACCTAAGAAGGACACAATCTATGGGAATCCAACTGGACCAGAAGATCATAATCCTTTACATGCTATCATGGGGTAAAGAAGCTGTGAATCACTTCCATCTTGGTGATGATATGGACCCTGAACTCAGGCAGCTAGCACAATCTCTGATCGATACTAAGGTGAAGGAGATCTCCAACCAAGAGCCACTTAAGTTGTAGGTGCTTAATGAAATCATGATTGAAGAAAGACTTTCCGGGCTTGTGCCACATATTAATCATCTCAGGACCTATCCTTAATGTGATTAATAGGGTTTTATTATAAGGGCAGTTAATGGGGTTGGTTACTAACTATGGGTAAGGGTTCATTACCATTTTTGCACTAGGGTTAAAGGGCCACTACATTGTATTTGCACTAAGGGAAATGGGAGGTGGGTTAGTTTGTATTTAGTTGTTAAGTTTTTTATAATCATATGTTAATGAGGAATTAGCTATATGATATCACTGATTGATTGGCTATTTTTAGGTTAAGTAATTGTAGTTAAATAGTTGTGTTAAGTTAGTATGTTAAGGTTTATAGGTTAAGATTTACTAACAATCATATTATGTCATTAGATGTAAATTTCATTCCTGGCTTGCTTCTGCTTTCGCATTGCTAACCTACAACAAGACTACCTCACCCACTACCCCTCCCCTATTCTACCTCAACACATACTACCTCACATTTGATTTTTCTTGATTGCTTTTCAAGGAGCATACTACTA \ No newline at end of file diff --git a/andv/NC_003467.2.fasta b/andv/NC_003467.2.fasta deleted file mode 100644 index 7e8d592..0000000 --- a/andv/NC_003467.2.fasta +++ /dev/null @@ -1 +0,0 @@ -TAGTAGTAGACTCCGCAAGAAGAAGCAAAAAATTAAAGAAGTGAGTTTAAAATGGAAGGGTGGTATCTGGTTGTTCTTGGAGTCTGCTATACGCTGACACTGGCAATGCCCAAGACCATTTATGAGCTTAAAATGGAATGCCCGCACACTGTGGGTCTCGGTCAAGGTTACATCATTGGCTCAACAGAACTAGGTTTGATCTCAATTGAGGCTGCATCTGATATAAAGCTCGAGAGCTCTTGCAATTTTGATCTTCATACAACATCTATGGCCCAGAAGAGTTTCACCCAAGTTGAATGGAGAAAGAAAAGTGACACAACTGATACCACAAATGCTGCGTCCACTACCTTTGAAGCACAAACTAAAACTGTTAACCTTAGAGGGACTTGTATACTGGCACCTGAACTCTATGATACATTGAAGAAAGTAAAAAAGACAGTCCTGTGCTATGATCTAACATGTAATCAAACACATTGTCAGCCAACTGTCTATCTGATTGCACCTGTATTGACATGCATGTCAATAAGAAGTTGTATGGCTAGTGTGTTTACAAGCAGGATTCAGGTGATTTATGAAAAGACACATTGTGTAACAGGTCAGCTGATTGAGGGTCAGTGTTTCAACCCAGCACACACATTGACATTATCTCAGCCTGCTCACACTTATGATACTGTCACCCTTCCTATCTCTTGTTTTTTCACACCAAAGAAGTCGGAGCAACTAAAAGTTATAAAAACATTTGAAGGAATTCTGACGAAGACAGGTTGCACGGAGAATGCATTGCAGGGTTATTATGTGTGTTTTTTAGGGAGTCATTCAGAACCTTTAATTGTTCCGAGTTTGGAGGACATACGGTCTGCTGAAGTTGTTAGTAGGATGCTTGTACACCCTAGGGGAGAAGACCATGATGCCATACAGAATTCACAAAGTCACTTAAGAATAGTGGGACCTATCACAGCAAAAGTGCCATCAACTAGTTCCACAGATACCCTAAAGGGGACAGCCTTTGCAGGCGTCCCAATGTATAGCTCTTTATCTACACTAGTCAGAAATGCAGACCCAGAATTTGTATTTTCTCCAGGTATAGTACCTGAATCTAATCACAGTACATGTGATAAGAAGACAGTACCTATCACATGGACAGGCTACCTACCAATATCAGGTGAGATGGAAAAAGTGACTGGATGTACAGTTTTTTGTACACTAGCAGGACCTGGTGCTAGTTGTGAGGCCTATTCTGAAAATGGTATATTTAACATCAGTTCTCCAACATGTCTTGTAAACAAAGTCCAAAGATTTCGTGGATCTGAACAGAAAATAAATTTTATCTGTCAGCGGGTAGATCAGGATGTTGTTGTATACTGCAATGGGCAAAAGAAAGTCATATTAACCAAAACTTTGGTTATTGGGCAGTGTATTTATACATTCACAAGCCTATTTTCATTGATGCCTGATGTAGCCCACTCATTGGCTGTAGAATTATGTGTCCCGGGATTACATGGATGGGCCACTGTCATGCTTCTATCAACATTCTGCTTTGGGTGGGTCTTGATTCCTGCGGTCACATTAATAATATTAAAGTGTCTAAGGGTTTTGACGTTTTCTTGTTCCCATTACACTAATGAGTCAAAATTTAAATTCATCCTGGAAAAAGTTAAAATTGAATACCAAAAGACTATGGGATCAATGGTGTGCGATGTATGTCATCATGAGTGTGAAACAGCAAAAGAACTTGAATCACATAGACAGAGTTGTATCAATGGACAATGTCCTTATTGCATGACAATAACTGAAGCAACTGAAAGTGCCTTGCAAGCCCATTATTCCATTTGTAAATTGACAGGAAGATTTCAGGAGGCACTGAAAAAGTCACTTAAAAAGCCAGAGGTAAAAAAAGGTTGTTACAGAACACTCGGGGTATTTAGATATAAAAGTAGATGTTATGTGGGTTTGGTATGGTGCCTATTGTTGACATGTGAAATTGTTATTTGGGCCGCAAGTGCAGAGACTCCACTAATGGAGTCAGGCTGGTCAGATACGGCTCATGGTGTTGGTGAGATTCCAATGAAGACAGACCTCGAGCTGGACTTTTCACTGCCTTCTTCATCCTCTTACAGTTATAGGAGAAAGCTCACAAACCCAGCCAATAAAGAAGAGTCTATTCCCTTCCACTTCCAGATGGAAAAACAAGTAATTCATGCTGAAATCCAACCCCTGGGTCATTGGATGGATGCGACATTTAATATTAAGACTGCATTTCATTGTTATGGTGCATGCCAGAAATACTCTTATCCATGGCAGACATCTAAGTGCTTCTTTGAAAAGGACTACCAGTATGAAACAGGCTGGGGCTGTAATCCTGGTGACTGCCCAGGGGTTGGGACTGGATGCACTGCTTGTGGTGTTTATCTCGATAAACTAAAATCTGTTGGGAAGGCCTATAAGATAATTTCTTTAAAATATACCAGAAAGGTTTGTATTCAGTTAGGAACAGAACAAACTTGCAAGCATATTGATGCAAATGATTGTTTAGTGACACCATCTGTGAAAGTTTGCATAGTGGGCACAGTTTCAAAACTTCAACCATCTGATACTCTTTTGTTCTTAGGTCCACTAGAACAAGGGGGAATCATTCTTAAGCAATGGTGCACAACATCATGTGCATTTGGGGACCCTGGTGATATCATGTCCACTCCCAGTGGTATGAGGTGTCCAGAGCACACTGGATCATTTAGGAAAATTTGCGGTTTTGCTACTACACCAGTTTGTGAATATCAAGGAAATACCATTTCTGGATATAAAAGAATGATGGCAACAAAAGATTCATTCCAATCATTTAACTTAACAGAACCTCACATCACAACAAACAAGCTTGAATGGATCGACCCAGATGGGAATACAAGAGACCACGTAAACCTTGTCTTAAATAGAGATGTCTCATTTCAGGATTTAAGTGATAACCCCTGTAAAGTAGACCTACACACACAAGCAATAGAAGGGGCATGGGGTTCTGGTGTAGGGTTTACACTCACATGTACTGTCGGATTAACAGAGTGCCCAAGTTTTATGACATCAATTAAGGCATGTGACCTAGCTATGTGTTATGGATCAACAGTAACAAACCTTGCCAGGGGCTCTAATACAGTGAAAGTAGTTGGTAAAGGAGGCCATTCAGGGTCCTCATTTAAATGCTGTCATGATACAGATTGCTCCTCTGAAGGTTTACTTGCATCAGCCCCTCATCTTGAGAGGGTAACAGGATTCAATCAAATTGATTCAGATAAGGTTTATGATGATGGTGCACCACCTTGCACATTCAAATGCTGGTTCACTAAGTCAGGTGAGTGGCTTCTTGGGATCTTAAACGGGAATTGGATTGTTGTTGTAGTGCTTGTTGTGATACTCATTCTCTCTATCATAATGTTCAGTGTTTTGTGTCCCAGGAGAGGGCACAAGAAAACTGTCTAAGCATTGACCTCAACTCCTACATTAGATCATATACATTTATGCACTTCCTCATATTTAGCTGCACTAAGATATTAATAAACTCTAGTTATTGACTTTATAAGATTATTATGGAACTAACCTCACTTAAAAAAAACAAATACTTTACTCATATATAACTCCATATTCTCTTACCGAGGCTTTTGTTCCTGCGGAGCATACTACTA \ No newline at end of file diff --git a/andv/NC_003468.2.fasta b/andv/NC_003468.2.fasta deleted file mode 100644 index 41776d0..0000000 --- a/andv/NC_003468.2.fasta +++ /dev/null @@ -1 +0,0 @@ -TAGTAGTAGACTCCGGGATAGAAAAAGTTAGAAAAATGGAAAAGTATAGAGAGATTCATCAGAGAGTTAGGGACCTTGCACCTGGAACGGTATCAGCATTAGAATGCATAGATCTACTGGATAGGCTCTACGCTGTCAGACATGACCTGGTTGACCAGATGATAAAACATGACTGGTCTGATAATAAAGATGTAGAAAGACCTATAGGTCAAGTTTTACTGATGGCTGGCATACCTAATGATATTATACAAGGCATGGAGAAGAAGATTATACCAAATAGCCCTTCTGGACAAGTATTGAAAAGCTTTTTCCGAATGACACCAGATAATTATAAAATTACAGGTAACTTGATTGAGTTTATTGAAGTGACTGTAACAGCTGATGTGTCACGAGGTATTAGGGAGAAGAAAATAAAGTATGAAGGAGGCCTCCAATTTGTTGAGCACTTACTGGAAACTGAATCAAGGAAGGGTAATATACCGCAACCTTATAAAATAACATTCTCAGTGGTTGCAGTTAAAACAGATGGATCAAACATCTCGACTCAGTGGCCCAGTCGGAGGAACGATGGGGTAGTTCAGCACATGCGTCTAGTCCAAGCTGATATAAATTATGTCAGAGAGCATTTAATAAAGTTAGATGAGAGAGCATCTTTGGAGGCAATGTTTAACTTAAAGTTCCATGTATCAGGCCCTAAACTGAGATACTTTAACATCCCTGATTATAGACCACAGCAGCTATGTGAACCACGGATTGACAACTTAATACAATATTGCAAGAATTGGTTGACAAAAGAACATAAGTTTGTATTCAAAGAAGTCAGTGGAGCTAATGTGATTCAAGCATTTGAGAGTCATGAACAGTTACATTTACAGAAATACAACGAATCACGAAAACCAAGAAATTTTTTACTCTTGCAGCTTACAGTGCAAGGGGCATATCTACCATCAACAATCAGTTCTGACCAGTGCAATACTAGGATTGGGTGTCTAGAAATATCAAAAAACCAACCAGAAACACCAGTACAGATGCTTGCATTGGATATATCTTATAAGTATCTGAGTCTTACAAGGGATGAGTTGATCAATTATTATAGCCCTAGAGTGCACTTTCAATCGAGCCCTAATGTGAAGGAACCAGGGACACTGAAGTTAGGATTATCACAATTAAATCCACTCTCTAAATCAATTCTTGACAATGTTGGAAAGCATAAAAAGGATAAAGGATTATTTGGTGAGATCATAGATAGCATAAATGTGGCAAGTCAAATACAGATCAATGCATGTGCAAAAATAATTGAGCAGATCTTATCAAATCTTGAAATAAACATTGGAGAAATAAATGCTAGTATGCCTTCTCCTAATAAGACAACAGGTGTAGATGACCTGTTAAATAAATTTTATGATAATGAGCTTGGTAAATATATGTTATCCATTCTGAGGAAAACAGCAGCATGGCATATAGGCCATCTAGTCAGAGATATCACAGAAAGTTTAATTGCACATGCTGGGCTGCGCCGTTCTAAATATTGGTCAGTACATGCATATGACCATGGGAATGTAATTTTGTTTATCTTGCCATCAAAGTCACTAGAGGTAGTAGGTTCTTATATAAGGTATTTCACAGTATTTAAAGATGGTATAGGGTTGATAGACGCAGATAATATTGATTCTAAGGCCGAAATTGATGGTGTCACCTGGTGTTATTCTAAGGTCATGAGTATTGATTTAAACAGGTTATTGGCTTTGAACATAGCTTTTGAGAAGTCACTTCTTGCCACGGCTACATGGTTCCAATATTATACTGAAGACCAAGGCCATTTTCCCCTTCAACATGCATTAAGGTCAATCTTTTCTTTCCACTTTTTACTCTGTGTGTCACAAAAGATGAAGCTATGTGCAATATTTGATAACCTTCGTTATCTGATACCATCAGTAACATCTTTGTACTCTGGGTACGAGTTGTTAATAGAAAAATTCTTTGAGAGACCATTTAAGAGTTCACTGGATGTATACCTTTATTCTATCATAAAATCTCTATTAATTAGTTTGGCACAAAATAATAAAGTTCGATTTTACTCAAGAGTTCGTTTGTTAGGATTGACAGTTGATCACTCCACGGTCGGAGCAAGTGGTGTTTACCCCTCTTTAATGTCCCGTGTTGTTTACAAACATTACAGAAGTTTAATCTCTGAAGCTACAACTTGTTTTTTCTTATTTGAAAAGGGTTTGCATGGGAATTTACCAGAAGAGGCTAAAATACATCTTGAAACCATTGAATGGGCTCGGAAGTTCCAGGAGAAAGAAAAACAATATGGTGATATTCTTCTAAAGGAAGGCTATACAATTGAATCTGTAATCAATGGAGAAGTTGATGTAGAACAACAGCTTTTTTGTCAGGAGGTCTCAGAGCTAAGTGCACAAGAGCTCAACAAATATTTACAGGCAAAATCTCAAGTTTTATGTGCTAATATCATGAATAAACACTGGGACAAACCATATTTCAGTCAAACACGCAATATCAGTCTCAAGGGAATGTCTGGGGCATTGCAAGAGGATGGACATTTAGCTGCTAGTGTGACACTGATTGAAGCAATTAGGTTTTTAAATAGATCACAAACCAATCCAAATGTTATTGATATGTATGAGCAGACTAAACAATCAAAGGCACAAGCTAGGATTGTTAGGAAATACCAGAGAACAGAAGCAGATAGAGGATTTTTTATCACAACATTACCAACTAGGGTGCGATTAGAAATAATAGAAGATTATTTCGATGCAATTGCAAAGGTTGTGCCTGAAGAATATATTTCTTATGGTGGGGATAAAAAAGTTCTAAATATTCAGAATGCACTAGAGAAAGCACTTAGATGGGCATCTGGAGTATCAGAAATTACAACAAGCACTGGTAAAAGCATCAAGTTTAAGCGGAAATTAATGTATGTTAGTGCTGATGCCACAAAATGGTCACCAGGAGATAATTCTGCTAAGTTTAGGAGATTTACACAAGCAATATATGATGGCTTATCAGACAACAAACTGAAATGTTGTGTTGTTGATGCATTACGTAACATTTATGAGACTGAATTTTTTATGTCCAGGAAATTACACCGATATATTGATAGTATGGAAAATCATTCAGATGCGGTTGAAGATTTCTTGGCATTTTTCTCAAATGGAGTCTCAGCCAATGTAAAGGGAAACTGGCTTCAAGGGAACTTAAATAAATGCTCATCATTATTTGGTGCTGCTGTCTCATTACTTTTTCGGGAGGTCTGGAAACAATTGTTTCCAGAATTAGAGTGTTTTTTTGAATTTGCACATCATTCAGATGATGCATTGTTCATTTATGGCTATCTGGAGCCTGAAGATGATGGAACAGATTGGTTTTTGTATGTATCACAGCAGATACAGGCAGGAAACTTTCATTGGCATGCTATAAATCAAGAGATGTGGAAGAGCATGTTTAATCTACATGAGCACTTACTATTAATGGGTTCTATTAAAGTGTCACCTAAGAAGACAACAGTATCACCTACTAATGCAGAATTTCTTTCTACTTTTTTTGAAGGTTGTGCTGTGTCAATCCCTTTTGTTAAAATCTTACTGGGTTCATTATCAGATCTTCCTGGGTTAGGTTTCTTTGATGATTTAGCAGCAGCACAAAGCAGATGTGTAAAGTCACTAGATTTGGGTGCTTGCCCACAATTAGCTCAACTAGCTATAGTATTATGCACAAGCAAAGTTGAGAGGTTGTATGGTACTGCTGATGGAATGGTAAACTCTCCAACAGCATTCCTTAAGGTGAATAAAGCACACGTACCAGTACCACTTGGTGGTGATGGCTCAATGTCTATTATGGAGCTTGCAACAGCTGGTTTTGGGATGGCAGATAAGAATATTTTAAAAAATGCATTCATATCTTATAAGCATACTCGTAGAGATGGTGATAGGTACGTATTGGGTTTATTTAAATTTTTGATGTCATTAAGTGAGGATGTATTCCAGCACGACCGATTGGGTGAGTTTAGTTTTGTAGGTAAAGTTCAATGGAAAGTGTTCACTCCTAAAGCTGAATTTGAATTTCATGATCAATTTTCACATAATTATTTATTAGAGTGGACACGTCAACATCCTGTGTATGACTATATTATTCCTAGAAATAGAGATAATTTGCTTGTATACCTTGTAAGAAAGTTGAATGATCCTAGCATCATTACAGCTATGACTATGCAGTCACCATTACAACTTCGTTTCCGTATGCAAGCAAAGCAACATATGAAAGTATGCCGGTATGAAGGTGAATGGGTCACATTCAGGGAGGTACTTGCTGCAGCTGATAGTTTTGCTACGAGTTACCAACCTACTGAAAGGGACATGGATCTCTTTAATACACTTGTAAGTTGTACATTTTCTAAAGAGTATGCTTGGAAAGACTTTTTAAATGAAGTAAGGTGTGAGGTCTTAACAACAAGACATGTACATAGGCCTAAAATTGCTAGGACATTCACTGTTAGAGAAAAGGACCAGGCTATACAAAATCCAATAAATTCGGTGATTGGCTATAAGTATGCTCTTACAGTGGATGAAGTCAGTGATGTTCTTGATAGTGCATTCTTCCCAGAGTCTCTATCTGCAGACTTACAGGTTATGAAAGATGGAGTTTACAGAGAATTAGGACTTGATATAAGTTCTCCTGAAGTCCTAAAACGCATAGCACCACTATTATATAAGGCAGGAAGGTCACGTGTTGTTATTGTGGAAGGAAATGTAGAAGGGACAGCTGAGTCAATCTGTAGTTATTGGCTCAAGACAATGTCACTGATTAAAACAATCAGAGTAAGACCTAAGAAGGAGGTACTGAAAGCTATGTCTTTATATAGTGTTAAAGAAAATATTGGATTGCAGGATGATATTGCAGCAACTCGACTATGCATAGAAATCTGGAGATGGTGTAAGGCAAATGAACAGGATGTTAAAGAATGGCTAACATCTCTGTACTTTGAAAAACAGACATTGATGGATTGGGTAGAAAGGTTTAGAAGGAAAGGAGTTGTTCCTATTGATCCTGAAATACAATGTATTGGCCTACTCTTATATGATGTATTAGGTTATAAAAGTGTGTTACAAATGCAAGCAAACCGAAGAGCCTATTCAGGTAAGCAATATGATGCATACTGTGTGCAAACATATAACGAGGAAACAAAACTATATGAAGGTGACCTTCGTGTTACTTTTAATTTTGGTTTAGATTGTGCAAGGTTAGAAGTTTTTTGGGATAAAAAAGAGTATATCTTAGAGACATCTATCACCCAACGACATGTGTTGCGGTTACTGATGGAAGAAGTGTCACAAGAATTAATTAGATGTGGAATGAGATTCAAAACAGAGCAAGTCAATCAAACTCGGAGCTTAGTGTTATTCAAAACAGAGGCTGGTTTTGAATGGGGTAAGCCTAATGTGCCATGTATTGTATATAAACACTGTGTCTTGAGAACTGGGCTTCGTACGAAACAGCCAATTAATAAAGAGTTCATGATAAATGTACAAAGTGATGGTTTCCGTGCAATAGCACAGATGGATATTGAGAGTCCACGGTTCTTGTTAGCACATGCATATCATACACTGCGTGATATTAGATATCAAGCAGTGCAGGCAGTAGGGAATGTATGGTTTAAAACAGAACAGCACAAACTATTTATTAACCCAATTATATCATCAGGGCTTTTAGAAAACTTTATGAAAGGCTTACCTGCTGCCATACCTCCTGCTGCATATTCCCTCATAATGAACAAGGCTAAGATTTCTGTGGATTTGTTTATGTTCAATGAGCTATTAGCACTTATAAATAGGAATAATATCCTCAACCTTGATGGGATTGAAGAAACATCTGAAGGTTATAGTACTGTGACATCAATGTCTAGCAAGCAGTGGTCTGAAGAGATGAGTTTAATGTCTGATGATGATATTGATGATATGGAGGACTTTACTATAGCACTGGATGATATTGACTTTGAACAAATAAATTTGGAAGAGGATATACAACACTTTCTGCAGGATGAATCAGCATATGTTGGTGATTTATTGATTCAGACAGAAGACATTGAGGTTAAAAAGATACGTGGGGTGACAAGAGTATTAGAGCCAGTCAAGCTATTAAAAAGCTGGGTTTCTAAAGGCCTTGCTATAGACAAAGTATACAATCCTATCGGGATAATCTTAATGGCAAGATACATGTCAAAAACATACAATTTCAGTTCAACACCTCTTGCACTATTAAATCCATATGACTTGACAGAACTTGAAAGTGTTGTAAAGGGATGGGGAGAAACTGTAAATGATCGATTCAAAGATTTAGATATTGAGGCACAAACAGTTGTTAAAGAAAAGGGTGTACAGCCAGAAGATGTACTCCCTGATTCATTATTCTCTTTCAGGCATGTTGATGTTTTGCTGCGAAGGTTGTTCCCGCGTGACCCTGTATCAACATTCTATTAGTGGATTTTATACCTTATTCATACAGTATGTATATTGTAGTGTTCTTTTCCCGGAGCATACTACTA \ No newline at end of file diff --git a/andv/genes/GPC.fasta b/andv/genes/GPC.fasta deleted file mode 100644 index fdb4124..0000000 --- a/andv/genes/GPC.fasta +++ /dev/null @@ -1 +0,0 @@ -MEGWYLVVLGVCYTLTLAMPKTIYELKMECPHTVGLGQGYIIGSTELGLISIEAASDIKLESSCNFDLHTTSMAQKSFTQVEWRKKSDTTDTTNAASTTFEAQTKTVNLRGTCILAPELYDTLKKVKKTVLCYDLTCNQTHCQPTVYLIAPVLTCMSIRSCMASVFTSRIQVIYEKTHCVTGQLIEGQCFNPAHTLTLSQPAHTYDTVTLPISCFFTPKKSEQLKVIKTFEGILTKTGCTENALQGYYVCFLGSHSEPLIVPSLEDIRSAEVVSRMLVHPRGEDHDAIQNSQSHLRIVGPITAKVPSTSSTDTLKGTAFAGVPMYSSLSTLVRNADPEFVFSPGIVPESNHSTCDKKTVPITWTGYLPISGEMEKVTGCTVFCTLAGPGASCEAYSENGIFNISSPTCLVNKVQRFRGSEQKINFICQRVDQDVVVYCNGQKKVILTKTLVIGQCIYTFTSLFSLMPDVAHSLAVELCVPGLHGWATVMLLSTFCFGWVLIPAVTLIILKCLRVLTFSCSHYTNESKFKFILEKVKIEYQKTMGSMVCDVCHHECETAKELESHRQSCINGQCPYCMTITEATESALQAHYSICKLTGRFQEALKKSLKKPEVKKGCYRTLGVFRYKSRCYVGLVWCLLLTCEIVIWAASAETPLMESGWSDTAHGVGEIPMKTDLELDFSLPSSSSYSYRRKLTNPANKEESIPFHFQMEKQVIHAEIQPLGHWMDATFNIKTAFHCYGACQKYSYPWQTSKCFFEKDYQYETGWGCNPGDCPGVGTGCTACGVYLDKLKSVGKAYKIISLKYTRKVCIQLGTEQTCKHIDANDCLVTPSVKVCIVGTVSKLQPSDTLLFLGPLEQGGIILKQWCTTSCAFGDPGDIMSTPSGMRCPEHTGSFRKICGFATTPVCEYQGNTISGYKRMMATKDSFQSFNLTEPHITTNKLEWIDPDGNTRDHVNLVLNRDVSFQDLSDNPCKVDLHTQAIEGAWGSGVGFTLTCTVGLTECPSFMTSIKACDLAMCYGSTVTNLARGSNTVKVVGKGGHSGSSFKCCHDTDCSSEGLLASAPHLERVTGFNQIDSDKVYDDGAPPCTFKCWFTKSGEWLLGILNGNWIVVVVLVVILILSIIMFSVLCPRRGHKKTV* \ No newline at end of file diff --git a/andv/genes/N.fasta b/andv/genes/N.fasta deleted file mode 100644 index 838059f..0000000 --- a/andv/genes/N.fasta +++ /dev/null @@ -1 +0,0 @@ -MSTLQELQENITAHEQQLVTARQKLKDAEKAVEVDPDDVNKSTLQSRRAAVSTLETKLGELKRQLADLVAAQKLATKPVDPTGLEPDDHLKEKSSLRYGNVLDVNSIDLEEPSGQTADWKAIGAYILGFAIPIILKALYMLSTRGRQTVKDNKGTRIRFKDDSSFEEVNGIRKPKHLYVSMPTAQSTMKAEEITPGRFRTIACGLFPAQVKARNIISPVMGVIGFGFFVKDWMDRIEEFLAAECPFLPKPKVASEAFMSTNKMYFLNRQRQVNESKVQDIIDLIDHAETESATLFTEIATPHSVWVFACAPDRCPPTALYVAGVPELGAFFSILQDMRNTIMASKSVGTAEEKLKKKSAFYQSYLRRTQSMGIQLDQKIIILYMLSWGKEAVNHFHLGDDMDPELRQLAQSLIDTKVKEISNQEPLKL* \ No newline at end of file diff --git a/andv/genes/NSs.fasta b/andv/genes/NSs.fasta deleted file mode 100644 index d2c888c..0000000 --- a/andv/genes/NSs.fasta +++ /dev/null @@ -1 +0,0 @@ -MPRRQWRWTRMTLTRAHYKVDGQLCLHWRPNSENLRGNLQIWWQLKNWLQNQLIQQGLSLMII* \ No newline at end of file diff --git a/andv/genes/RdRp.fasta b/andv/genes/RdRp.fasta deleted file mode 100644 index 22b6ddb..0000000 --- a/andv/genes/RdRp.fasta +++ /dev/null @@ -1 +0,0 @@ -MEKYREIHQRVRDLAPGTVSALECIDLLDRLYAVRHDLVDQMIKHDWSDNKDVERPIGQVLLMAGIPNDIIQGMEKKIIPNSPSGQVLKSFFRMTPDNYKITGNLIEFIEVTVTADVSRGIREKKIKYEGGLQFVEHLLETESRKGNIPQPYKITFSVVAVKTDGSNISTQWPSRRNDGVVQHMRLVQADINYVREHLIKLDERASLEAMFNLKFHVSGPKLRYFNIPDYRPQQLCEPRIDNLIQYCKNWLTKEHKFVFKEVSGANVIQAFESHEQLHLQKYNESRKPRNFLLLQLTVQGAYLPSTISSDQCNTRIGCLEISKNQPETPVQMLALDISYKYLSLTRDELINYYSPRVHFQSSPNVKEPGTLKLGLSQLNPLSKSILDNVGKHKKDKGLFGEIIDSINVASQIQINACAKIIEQILSNLEINIGEINASMPSPNKTTGVDDLLNKFYDNELGKYMLSILRKTAAWHIGHLVRDITESLIAHAGLRRSKYWSVHAYDHGNVILFILPSKSLEVVGSYIRYFTVFKDGIGLIDADNIDSKAEIDGVTWCYSKVMSIDLNRLLALNIAFEKSLLATATWFQYYTEDQGHFPLQHALRSIFSFHFLLCVSQKMKLCAIFDNLRYLIPSVTSLYSGYELLIEKFFERPFKSSLDVYLYSIIKSLLISLAQNNKVRFYSRVRLLGLTVDHSTVGASGVYPSLMSRVVYKHYRSLISEATTCFFLFEKGLHGNLPEEAKIHLETIEWARKFQEKEKQYGDILLKEGYTIESVINGEVDVEQQLFCQEVSELSAQELNKYLQAKSQVLCANIMNKHWDKPYFSQTRNISLKGMSGALQEDGHLAASVTLIEAIRFLNRSQTNPNVIDMYEQTKQSKAQARIVRKYQRTEADRGFFITTLPTRVRLEIIEDYFDAIAKVVPEEYISYGGDKKVLNIQNALEKALRWASGVSEITTSTGKSIKFKRKLMYVSADATKWSPGDNSAKFRRFTQAIYDGLSDNKLKCCVVDALRNIYETEFFMSRKLHRYIDSMENHSDAVEDFLAFFSNGVSANVKGNWLQGNLNKCSSLFGAAVSLLFREVWKQLFPELECFFEFAHHSDDALFIYGYLEPEDDGTDWFLYVSQQIQAGNFHWHAINQEMWKSMFNLHEHLLLMGSIKVSPKKTTVSPTNAEFLSTFFEGCAVSIPFVKILLGSLSDLPGLGFFDDLAAAQSRCVKSLDLGACPQLAQLAIVLCTSKVERLYGTADGMVNSPTAFLKVNKAHVPVPLGGDGSMSIMELATAGFGMADKNILKNAFISYKHTRRDGDRYVLGLFKFLMSLSEDVFQHDRLGEFSFVGKVQWKVFTPKAEFEFHDQFSHNYLLEWTRQHPVYDYIIPRNRDNLLVYLVRKLNDPSIITAMTMQSPLQLRFRMQAKQHMKVCRYEGEWVTFREVLAAADSFATSYQPTERDMDLFNTLVSCTFSKEYAWKDFLNEVRCEVLTTRHVHRPKIARTFTVREKDQAIQNPINSVIGYKYALTVDEVSDVLDSAFFPESLSADLQVMKDGVYRELGLDISSPEVLKRIAPLLYKAGRSRVVIVEGNVEGTAESICSYWLKTMSLIKTIRVRPKKEVLKAMSLYSVKENIGLQDDIAATRLCIEIWRWCKANEQDVKEWLTSLYFEKQTLMDWVERFRRKGVVPIDPEIQCIGLLLYDVLGYKSVLQMQANRRAYSGKQYDAYCVQTYNEETKLYEGDLRVTFNFGLDCARLEVFWDKKEYILETSITQRHVLRLLMEEVSQELIRCGMRFKTEQVNQTRSLVLFKTEAGFEWGKPNVPCIVYKHCVLRTGLRTKQPINKEFMINVQSDGFRAIAQMDIESPRFLLAHAYHTLRDIRYQAVQAVGNVWFKTEQHKLFINPIISSGLLENFMKGLPAAIPPAAYSLIMNKAKISVDLFMFNELLALINRNNILNLDGIEETSEGYSTVTSMSSKQWSEEMSLMSDDDIDDMEDFTIALDDIDFEQINLEEDIQHFLQDESAYVGDLLIQTEDIEVKKIRGVTRVLEPVKLLKSWVSKGLAIDKVYNPIGIILMARYMSKTYNFSSTPLALLNPYDLTELESVVKGWGETVNDRFKDLDIEAQTVVKEKGVQPEDVLPDSLFSFRHVDVLLRRLFPRDPVSTFY* \ No newline at end of file diff --git a/andv/nextclade/L/CHANGELOG.md b/andv/nextclade/L/CHANGELOG.md deleted file mode 100644 index 0f72c1e..0000000 --- a/andv/nextclade/L/CHANGELOG.md +++ /dev/null @@ -1,5 +0,0 @@ -# Changelog - -## 2026-05-08 - -Initial minimal dataset generated from NCBI GenBank reference annotation. diff --git a/andv/nextclade/L/README.md b/andv/nextclade/L/README.md deleted file mode 100644 index fcfadb1..0000000 --- a/andv/nextclade/L/README.md +++ /dev/null @@ -1,3 +0,0 @@ -# Andes virus L segment - -Minimal Nextclade dataset for Andes virus L segment using Andes virus reference. diff --git a/andv/nextclade/L/genome_annotation.gff3 b/andv/nextclade/L/genome_annotation.gff3 deleted file mode 100644 index 2671f79..0000000 --- a/andv/nextclade/L/genome_annotation.gff3 +++ /dev/null @@ -1,7 +0,0 @@ -##gff-version 3 -#!gff-spec-version 1.21 -#!processor NCBI annotwriter -##sequence-region NC_003468.2 1 6562 -##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1980456 -NC_003468.2 RefSeq region 1 6562 . + . ID=NC_003468.2:1..6562;Dbxref=taxon:1980456;Name=L;gbkey=Src;genome=genomic;mol_type=genomic RNA;old-name=Andes virus;segment=L;strain=Chile-9717869 -NC_003468.2 RefSeq CDS 36 6497 . + 0 Name=RdRp;gbkey=CDS;locus_tag=ANDVsLgp1;protein_id=NP_604473.1;product=RNA polymerase;ID=cds-NP_604473.1;Dbxref=GenBank:NP_604473.1,GeneID:991234 diff --git a/andv/nextclade/L/pathogen.json b/andv/nextclade/L/pathogen.json deleted file mode 100644 index 96758f5..0000000 --- a/andv/nextclade/L/pathogen.json +++ /dev/null @@ -1,39 +0,0 @@ -{ - "$schema": "https://raw.githubusercontent.com/nextstrain/nextclade/refs/heads/release/packages/nextclade-schemas/input-pathogen-json.schema.json", - "schemaVersion": "3.0.0", - "files": { - "reference": "reference.fasta", - "pathogenJson": "pathogen.json", - "genomeAnnotation": "genome_annotation.gff3", - "examples": "sequences.fasta", - "readme": "README.md", - "changelog": "CHANGELOG.md" - }, - "attributes": { - "name": "Andes virus L", - "reference name": "Andes virus segment L", - "reference accession": "NC_003468.2" - }, - "qc": { - "missingData": { - "enabled": true, - "missingDataThreshold": 2000, - "scoreBias": 500 - }, - "snpClusters": { - "enabled": false - }, - "mixedSites": { - "enabled": true, - "mixedSitesThreshold": 15 - }, - "frameShifts": { - "enabled": true, - "scoreWeight": 20 - }, - "stopCodons": { - "enabled": true, - "scoreWeight": 50 - } - } -} diff --git a/andv/nextclade/L/reference.fasta b/andv/nextclade/L/reference.fasta deleted file mode 100644 index 30c0f8f..0000000 --- a/andv/nextclade/L/reference.fasta +++ /dev/null @@ -1,111 +0,0 @@ ->NC_003468.2 Andes virus segment L, complete genome -TAGTAGTAGACTCCGGGATAGAAAAAGTTAGAAAAATGGAAAAGTATAGAGAGATTCATC -AGAGAGTTAGGGACCTTGCACCTGGAACGGTATCAGCATTAGAATGCATAGATCTACTGG -ATAGGCTCTACGCTGTCAGACATGACCTGGTTGACCAGATGATAAAACATGACTGGTCTG -ATAATAAAGATGTAGAAAGACCTATAGGTCAAGTTTTACTGATGGCTGGCATACCTAATG -ATATTATACAAGGCATGGAGAAGAAGATTATACCAAATAGCCCTTCTGGACAAGTATTGA -AAAGCTTTTTCCGAATGACACCAGATAATTATAAAATTACAGGTAACTTGATTGAGTTTA -TTGAAGTGACTGTAACAGCTGATGTGTCACGAGGTATTAGGGAGAAGAAAATAAAGTATG -AAGGAGGCCTCCAATTTGTTGAGCACTTACTGGAAACTGAATCAAGGAAGGGTAATATAC -CGCAACCTTATAAAATAACATTCTCAGTGGTTGCAGTTAAAACAGATGGATCAAACATCT -CGACTCAGTGGCCCAGTCGGAGGAACGATGGGGTAGTTCAGCACATGCGTCTAGTCCAAG -CTGATATAAATTATGTCAGAGAGCATTTAATAAAGTTAGATGAGAGAGCATCTTTGGAGG -CAATGTTTAACTTAAAGTTCCATGTATCAGGCCCTAAACTGAGATACTTTAACATCCCTG -ATTATAGACCACAGCAGCTATGTGAACCACGGATTGACAACTTAATACAATATTGCAAGA -ATTGGTTGACAAAAGAACATAAGTTTGTATTCAAAGAAGTCAGTGGAGCTAATGTGATTC -AAGCATTTGAGAGTCATGAACAGTTACATTTACAGAAATACAACGAATCACGAAAACCAA -GAAATTTTTTACTCTTGCAGCTTACAGTGCAAGGGGCATATCTACCATCAACAATCAGTT -CTGACCAGTGCAATACTAGGATTGGGTGTCTAGAAATATCAAAAAACCAACCAGAAACAC -CAGTACAGATGCTTGCATTGGATATATCTTATAAGTATCTGAGTCTTACAAGGGATGAGT -TGATCAATTATTATAGCCCTAGAGTGCACTTTCAATCGAGCCCTAATGTGAAGGAACCAG -GGACACTGAAGTTAGGATTATCACAATTAAATCCACTCTCTAAATCAATTCTTGACAATG -TTGGAAAGCATAAAAAGGATAAAGGATTATTTGGTGAGATCATAGATAGCATAAATGTGG -CAAGTCAAATACAGATCAATGCATGTGCAAAAATAATTGAGCAGATCTTATCAAATCTTG -AAATAAACATTGGAGAAATAAATGCTAGTATGCCTTCTCCTAATAAGACAACAGGTGTAG -ATGACCTGTTAAATAAATTTTATGATAATGAGCTTGGTAAATATATGTTATCCATTCTGA -GGAAAACAGCAGCATGGCATATAGGCCATCTAGTCAGAGATATCACAGAAAGTTTAATTG -CACATGCTGGGCTGCGCCGTTCTAAATATTGGTCAGTACATGCATATGACCATGGGAATG -TAATTTTGTTTATCTTGCCATCAAAGTCACTAGAGGTAGTAGGTTCTTATATAAGGTATT -TCACAGTATTTAAAGATGGTATAGGGTTGATAGACGCAGATAATATTGATTCTAAGGCCG -AAATTGATGGTGTCACCTGGTGTTATTCTAAGGTCATGAGTATTGATTTAAACAGGTTAT -TGGCTTTGAACATAGCTTTTGAGAAGTCACTTCTTGCCACGGCTACATGGTTCCAATATT -ATACTGAAGACCAAGGCCATTTTCCCCTTCAACATGCATTAAGGTCAATCTTTTCTTTCC -ACTTTTTACTCTGTGTGTCACAAAAGATGAAGCTATGTGCAATATTTGATAACCTTCGTT -ATCTGATACCATCAGTAACATCTTTGTACTCTGGGTACGAGTTGTTAATAGAAAAATTCT -TTGAGAGACCATTTAAGAGTTCACTGGATGTATACCTTTATTCTATCATAAAATCTCTAT -TAATTAGTTTGGCACAAAATAATAAAGTTCGATTTTACTCAAGAGTTCGTTTGTTAGGAT -TGACAGTTGATCACTCCACGGTCGGAGCAAGTGGTGTTTACCCCTCTTTAATGTCCCGTG -TTGTTTACAAACATTACAGAAGTTTAATCTCTGAAGCTACAACTTGTTTTTTCTTATTTG -AAAAGGGTTTGCATGGGAATTTACCAGAAGAGGCTAAAATACATCTTGAAACCATTGAAT -GGGCTCGGAAGTTCCAGGAGAAAGAAAAACAATATGGTGATATTCTTCTAAAGGAAGGCT -ATACAATTGAATCTGTAATCAATGGAGAAGTTGATGTAGAACAACAGCTTTTTTGTCAGG -AGGTCTCAGAGCTAAGTGCACAAGAGCTCAACAAATATTTACAGGCAAAATCTCAAGTTT -TATGTGCTAATATCATGAATAAACACTGGGACAAACCATATTTCAGTCAAACACGCAATA -TCAGTCTCAAGGGAATGTCTGGGGCATTGCAAGAGGATGGACATTTAGCTGCTAGTGTGA -CACTGATTGAAGCAATTAGGTTTTTAAATAGATCACAAACCAATCCAAATGTTATTGATA -TGTATGAGCAGACTAAACAATCAAAGGCACAAGCTAGGATTGTTAGGAAATACCAGAGAA -CAGAAGCAGATAGAGGATTTTTTATCACAACATTACCAACTAGGGTGCGATTAGAAATAA -TAGAAGATTATTTCGATGCAATTGCAAAGGTTGTGCCTGAAGAATATATTTCTTATGGTG -GGGATAAAAAAGTTCTAAATATTCAGAATGCACTAGAGAAAGCACTTAGATGGGCATCTG -GAGTATCAGAAATTACAACAAGCACTGGTAAAAGCATCAAGTTTAAGCGGAAATTAATGT -ATGTTAGTGCTGATGCCACAAAATGGTCACCAGGAGATAATTCTGCTAAGTTTAGGAGAT -TTACACAAGCAATATATGATGGCTTATCAGACAACAAACTGAAATGTTGTGTTGTTGATG -CATTACGTAACATTTATGAGACTGAATTTTTTATGTCCAGGAAATTACACCGATATATTG -ATAGTATGGAAAATCATTCAGATGCGGTTGAAGATTTCTTGGCATTTTTCTCAAATGGAG -TCTCAGCCAATGTAAAGGGAAACTGGCTTCAAGGGAACTTAAATAAATGCTCATCATTAT -TTGGTGCTGCTGTCTCATTACTTTTTCGGGAGGTCTGGAAACAATTGTTTCCAGAATTAG -AGTGTTTTTTTGAATTTGCACATCATTCAGATGATGCATTGTTCATTTATGGCTATCTGG -AGCCTGAAGATGATGGAACAGATTGGTTTTTGTATGTATCACAGCAGATACAGGCAGGAA -ACTTTCATTGGCATGCTATAAATCAAGAGATGTGGAAGAGCATGTTTAATCTACATGAGC -ACTTACTATTAATGGGTTCTATTAAAGTGTCACCTAAGAAGACAACAGTATCACCTACTA -ATGCAGAATTTCTTTCTACTTTTTTTGAAGGTTGTGCTGTGTCAATCCCTTTTGTTAAAA -TCTTACTGGGTTCATTATCAGATCTTCCTGGGTTAGGTTTCTTTGATGATTTAGCAGCAG -CACAAAGCAGATGTGTAAAGTCACTAGATTTGGGTGCTTGCCCACAATTAGCTCAACTAG -CTATAGTATTATGCACAAGCAAAGTTGAGAGGTTGTATGGTACTGCTGATGGAATGGTAA -ACTCTCCAACAGCATTCCTTAAGGTGAATAAAGCACACGTACCAGTACCACTTGGTGGTG -ATGGCTCAATGTCTATTATGGAGCTTGCAACAGCTGGTTTTGGGATGGCAGATAAGAATA -TTTTAAAAAATGCATTCATATCTTATAAGCATACTCGTAGAGATGGTGATAGGTACGTAT -TGGGTTTATTTAAATTTTTGATGTCATTAAGTGAGGATGTATTCCAGCACGACCGATTGG -GTGAGTTTAGTTTTGTAGGTAAAGTTCAATGGAAAGTGTTCACTCCTAAAGCTGAATTTG -AATTTCATGATCAATTTTCACATAATTATTTATTAGAGTGGACACGTCAACATCCTGTGT -ATGACTATATTATTCCTAGAAATAGAGATAATTTGCTTGTATACCTTGTAAGAAAGTTGA -ATGATCCTAGCATCATTACAGCTATGACTATGCAGTCACCATTACAACTTCGTTTCCGTA -TGCAAGCAAAGCAACATATGAAAGTATGCCGGTATGAAGGTGAATGGGTCACATTCAGGG -AGGTACTTGCTGCAGCTGATAGTTTTGCTACGAGTTACCAACCTACTGAAAGGGACATGG -ATCTCTTTAATACACTTGTAAGTTGTACATTTTCTAAAGAGTATGCTTGGAAAGACTTTT -TAAATGAAGTAAGGTGTGAGGTCTTAACAACAAGACATGTACATAGGCCTAAAATTGCTA -GGACATTCACTGTTAGAGAAAAGGACCAGGCTATACAAAATCCAATAAATTCGGTGATTG -GCTATAAGTATGCTCTTACAGTGGATGAAGTCAGTGATGTTCTTGATAGTGCATTCTTCC -CAGAGTCTCTATCTGCAGACTTACAGGTTATGAAAGATGGAGTTTACAGAGAATTAGGAC -TTGATATAAGTTCTCCTGAAGTCCTAAAACGCATAGCACCACTATTATATAAGGCAGGAA -GGTCACGTGTTGTTATTGTGGAAGGAAATGTAGAAGGGACAGCTGAGTCAATCTGTAGTT -ATTGGCTCAAGACAATGTCACTGATTAAAACAATCAGAGTAAGACCTAAGAAGGAGGTAC -TGAAAGCTATGTCTTTATATAGTGTTAAAGAAAATATTGGATTGCAGGATGATATTGCAG -CAACTCGACTATGCATAGAAATCTGGAGATGGTGTAAGGCAAATGAACAGGATGTTAAAG -AATGGCTAACATCTCTGTACTTTGAAAAACAGACATTGATGGATTGGGTAGAAAGGTTTA -GAAGGAAAGGAGTTGTTCCTATTGATCCTGAAATACAATGTATTGGCCTACTCTTATATG -ATGTATTAGGTTATAAAAGTGTGTTACAAATGCAAGCAAACCGAAGAGCCTATTCAGGTA -AGCAATATGATGCATACTGTGTGCAAACATATAACGAGGAAACAAAACTATATGAAGGTG -ACCTTCGTGTTACTTTTAATTTTGGTTTAGATTGTGCAAGGTTAGAAGTTTTTTGGGATA -AAAAAGAGTATATCTTAGAGACATCTATCACCCAACGACATGTGTTGCGGTTACTGATGG -AAGAAGTGTCACAAGAATTAATTAGATGTGGAATGAGATTCAAAACAGAGCAAGTCAATC -AAACTCGGAGCTTAGTGTTATTCAAAACAGAGGCTGGTTTTGAATGGGGTAAGCCTAATG -TGCCATGTATTGTATATAAACACTGTGTCTTGAGAACTGGGCTTCGTACGAAACAGCCAA -TTAATAAAGAGTTCATGATAAATGTACAAAGTGATGGTTTCCGTGCAATAGCACAGATGG -ATATTGAGAGTCCACGGTTCTTGTTAGCACATGCATATCATACACTGCGTGATATTAGAT -ATCAAGCAGTGCAGGCAGTAGGGAATGTATGGTTTAAAACAGAACAGCACAAACTATTTA -TTAACCCAATTATATCATCAGGGCTTTTAGAAAACTTTATGAAAGGCTTACCTGCTGCCA -TACCTCCTGCTGCATATTCCCTCATAATGAACAAGGCTAAGATTTCTGTGGATTTGTTTA -TGTTCAATGAGCTATTAGCACTTATAAATAGGAATAATATCCTCAACCTTGATGGGATTG -AAGAAACATCTGAAGGTTATAGTACTGTGACATCAATGTCTAGCAAGCAGTGGTCTGAAG -AGATGAGTTTAATGTCTGATGATGATATTGATGATATGGAGGACTTTACTATAGCACTGG -ATGATATTGACTTTGAACAAATAAATTTGGAAGAGGATATACAACACTTTCTGCAGGATG -AATCAGCATATGTTGGTGATTTATTGATTCAGACAGAAGACATTGAGGTTAAAAAGATAC -GTGGGGTGACAAGAGTATTAGAGCCAGTCAAGCTATTAAAAAGCTGGGTTTCTAAAGGCC -TTGCTATAGACAAAGTATACAATCCTATCGGGATAATCTTAATGGCAAGATACATGTCAA -AAACATACAATTTCAGTTCAACACCTCTTGCACTATTAAATCCATATGACTTGACAGAAC -TTGAAAGTGTTGTAAAGGGATGGGGAGAAACTGTAAATGATCGATTCAAAGATTTAGATA -TTGAGGCACAAACAGTTGTTAAAGAAAAGGGTGTACAGCCAGAAGATGTACTCCCTGATT -CATTATTCTCTTTCAGGCATGTTGATGTTTTGCTGCGAAGGTTGTTCCCGCGTGACCCTG -TATCAACATTCTATTAGTGGATTTTATACCTTATTCATACAGTATGTATATTGTAGTGTT -CTTTTCCCGGAGCATACTACTA diff --git a/andv/nextclade/L/reference.gb b/andv/nextclade/L/reference.gb deleted file mode 100644 index 338abc9..0000000 --- a/andv/nextclade/L/reference.gb +++ /dev/null @@ -1,185 +0,0 @@ -LOCUS NC_003468 6562 bp RNA linear VRL 13-AUG-2018 -DEFINITION Andes virus segment L, complete genome. -ACCESSION NC_003468 -VERSION NC_003468.2 -DBLINK BioProject: PRJNA485481 -KEYWORDS RefSeq. -SOURCE Orthohantavirus andesense - ORGANISM Orthohantavirus andesense - Viruses; Riboviria; Orthornavirae; Negarnaviricota; - Polyploviricotina; Bunyaviricetes; Elliovirales; Hantaviridae; - Mammantavirinae; Orthohantavirus. -REFERENCE 1 (bases 1 to 6562) - AUTHORS Meissner,J.D., Rowe,J.E., Borucki,M.K. and St Jeor,S.C. - TITLE Complete nucleotide sequence of a Chilean hantavirus - JOURNAL Virus Res. 89 (1), 131-143 (2002) - PUBMED 12367756 -REFERENCE 2 (bases 1 to 6562) - AUTHORS Meissner,J.D. and St. Jeor,S.C. - TITLE Hantavirus strain Andes 23 L segment sequence - JOURNAL Unpublished -REFERENCE 3 (bases 1 to 6562) - CONSRTM NCBI Genome Project - TITLE Direct Submission - JOURNAL Submitted (17-NOV-2010) National Center for Biotechnology - Information, NIH, Bethesda, MD 20894, USA -REFERENCE 4 (bases 1 to 6562) - AUTHORS Meissner,J.D. and St. Jeor,S.C. - TITLE Direct Submission - JOURNAL Submitted (02-OCT-2002) Microbiology, University of Nevada-Reno, - FA310/MS200, Reno, NV 89557, USA - REMARK Sequence update by submitter -REFERENCE 5 (bases 1 to 6562) - AUTHORS Meissner,J.D. and St. Jeor,S.C. - TITLE Direct Submission - JOURNAL Submitted (21-NOV-2001) Microbiology, University of Nevada-Reno, - FA310/MS200, Reno, NV 89557, USA - REMARK Sequence update by submitter -REFERENCE 6 (bases 1 to 6562) - AUTHORS Meissner,J.D. and St. Jeor,S.C. - TITLE Direct Submission - JOURNAL Submitted (03-AUG-2001) Microbiology, University of Nevada-Reno, - FA310/MS200, Reno, NV 89557, USA - REMARK Sequence update by submitter -REFERENCE 7 (bases 1 to 6562) - AUTHORS Meissner,J.D. and St. Jeor,S.C. - TITLE Direct Submission - JOURNAL Submitted (18-APR-2001) Microbiology, University of Nevada-Reno, - FA310/MS200, Reno, NV 89557, USA - REMARK Sequence update by submitter -REFERENCE 8 (bases 1 to 3362) - AUTHORS Meissner,J.D. and St. Jeor,S.C. - TITLE Direct Submission - JOURNAL Submitted (01-AUG-2000) Microbiology, University of Nevada-Reno, - FA310/MS200, Reno, NV 89557, USA -COMMENT PROVISIONAL REFSEQ: This record has not yet been subject to final - NCBI review. The reference sequence is identical to AF291704. - On Oct 2, 2002 this sequence version replaced NC_003468.1. - COMPLETENESS: full length. -FEATURES Location/Qualifiers - source 1..6562 - /organism="Orthohantavirus andesense" - /mol_type="genomic RNA" - /strain="Chile-9717869" - /db_xref="taxon:1980456" - /segment="L" - CDS 36..6497 - /ID="cds-NP_604473.1" - /Dbxref="GenBank:NP_604473.1,GeneID:991234" - /Name="RdRp" - /gbkey="CDS" - /locus_tag="RdRp" - /product="RNA polymerase" - /protein_id="NP_604473.1" -ORIGIN - 1 tagtagtaga ctccgggata gaaaaagtta gaaaaatgga aaagtataga gagattcatc - 61 agagagttag ggaccttgca cctggaacgg tatcagcatt agaatgcata gatctactgg - 121 ataggctcta cgctgtcaga catgacctgg ttgaccagat gataaaacat gactggtctg - 181 ataataaaga tgtagaaaga cctataggtc aagttttact gatggctggc atacctaatg - 241 atattataca aggcatggag aagaagatta taccaaatag cccttctgga caagtattga - 301 aaagcttttt ccgaatgaca ccagataatt ataaaattac aggtaacttg attgagttta - 361 ttgaagtgac tgtaacagct gatgtgtcac gaggtattag ggagaagaaa ataaagtatg - 421 aaggaggcct ccaatttgtt gagcacttac tggaaactga atcaaggaag ggtaatatac - 481 cgcaacctta taaaataaca ttctcagtgg ttgcagttaa aacagatgga tcaaacatct - 541 cgactcagtg gcccagtcgg aggaacgatg gggtagttca gcacatgcgt ctagtccaag - 601 ctgatataaa ttatgtcaga gagcatttaa taaagttaga tgagagagca tctttggagg - 661 caatgtttaa cttaaagttc catgtatcag gccctaaact gagatacttt aacatccctg - 721 attatagacc acagcagcta tgtgaaccac ggattgacaa cttaatacaa tattgcaaga - 781 attggttgac aaaagaacat aagtttgtat tcaaagaagt cagtggagct aatgtgattc - 841 aagcatttga gagtcatgaa cagttacatt tacagaaata caacgaatca cgaaaaccaa - 901 gaaatttttt actcttgcag cttacagtgc aaggggcata tctaccatca acaatcagtt - 961 ctgaccagtg caatactagg attgggtgtc tagaaatatc aaaaaaccaa ccagaaacac - 1021 cagtacagat gcttgcattg gatatatctt ataagtatct gagtcttaca agggatgagt - 1081 tgatcaatta ttatagccct agagtgcact ttcaatcgag ccctaatgtg aaggaaccag - 1141 ggacactgaa gttaggatta tcacaattaa atccactctc taaatcaatt cttgacaatg - 1201 ttggaaagca taaaaaggat aaaggattat ttggtgagat catagatagc ataaatgtgg - 1261 caagtcaaat acagatcaat gcatgtgcaa aaataattga gcagatctta tcaaatcttg - 1321 aaataaacat tggagaaata aatgctagta tgccttctcc taataagaca acaggtgtag - 1381 atgacctgtt aaataaattt tatgataatg agcttggtaa atatatgtta tccattctga - 1441 ggaaaacagc agcatggcat ataggccatc tagtcagaga tatcacagaa agtttaattg - 1501 cacatgctgg gctgcgccgt tctaaatatt ggtcagtaca tgcatatgac catgggaatg - 1561 taattttgtt tatcttgcca tcaaagtcac tagaggtagt aggttcttat ataaggtatt - 1621 tcacagtatt taaagatggt atagggttga tagacgcaga taatattgat tctaaggccg - 1681 aaattgatgg tgtcacctgg tgttattcta aggtcatgag tattgattta aacaggttat - 1741 tggctttgaa catagctttt gagaagtcac ttcttgccac ggctacatgg ttccaatatt - 1801 atactgaaga ccaaggccat tttccccttc aacatgcatt aaggtcaatc ttttctttcc - 1861 actttttact ctgtgtgtca caaaagatga agctatgtgc aatatttgat aaccttcgtt - 1921 atctgatacc atcagtaaca tctttgtact ctgggtacga gttgttaata gaaaaattct - 1981 ttgagagacc atttaagagt tcactggatg tataccttta ttctatcata aaatctctat - 2041 taattagttt ggcacaaaat aataaagttc gattttactc aagagttcgt ttgttaggat - 2101 tgacagttga tcactccacg gtcggagcaa gtggtgttta cccctcttta atgtcccgtg - 2161 ttgtttacaa acattacaga agtttaatct ctgaagctac aacttgtttt ttcttatttg - 2221 aaaagggttt gcatgggaat ttaccagaag aggctaaaat acatcttgaa accattgaat - 2281 gggctcggaa gttccaggag aaagaaaaac aatatggtga tattcttcta aaggaaggct - 2341 atacaattga atctgtaatc aatggagaag ttgatgtaga acaacagctt ttttgtcagg - 2401 aggtctcaga gctaagtgca caagagctca acaaatattt acaggcaaaa tctcaagttt - 2461 tatgtgctaa tatcatgaat aaacactggg acaaaccata tttcagtcaa acacgcaata - 2521 tcagtctcaa gggaatgtct ggggcattgc aagaggatgg acatttagct gctagtgtga - 2581 cactgattga agcaattagg tttttaaata gatcacaaac caatccaaat gttattgata - 2641 tgtatgagca gactaaacaa tcaaaggcac aagctaggat tgttaggaaa taccagagaa - 2701 cagaagcaga tagaggattt tttatcacaa cattaccaac tagggtgcga ttagaaataa - 2761 tagaagatta tttcgatgca attgcaaagg ttgtgcctga agaatatatt tcttatggtg - 2821 gggataaaaa agttctaaat attcagaatg cactagagaa agcacttaga tgggcatctg - 2881 gagtatcaga aattacaaca agcactggta aaagcatcaa gtttaagcgg aaattaatgt - 2941 atgttagtgc tgatgccaca aaatggtcac caggagataa ttctgctaag tttaggagat - 3001 ttacacaagc aatatatgat ggcttatcag acaacaaact gaaatgttgt gttgttgatg - 3061 cattacgtaa catttatgag actgaatttt ttatgtccag gaaattacac cgatatattg - 3121 atagtatgga aaatcattca gatgcggttg aagatttctt ggcatttttc tcaaatggag - 3181 tctcagccaa tgtaaaggga aactggcttc aagggaactt aaataaatgc tcatcattat - 3241 ttggtgctgc tgtctcatta ctttttcggg aggtctggaa acaattgttt ccagaattag - 3301 agtgtttttt tgaatttgca catcattcag atgatgcatt gttcatttat ggctatctgg - 3361 agcctgaaga tgatggaaca gattggtttt tgtatgtatc acagcagata caggcaggaa - 3421 actttcattg gcatgctata aatcaagaga tgtggaagag catgtttaat ctacatgagc - 3481 acttactatt aatgggttct attaaagtgt cacctaagaa gacaacagta tcacctacta - 3541 atgcagaatt tctttctact ttttttgaag gttgtgctgt gtcaatccct tttgttaaaa - 3601 tcttactggg ttcattatca gatcttcctg ggttaggttt ctttgatgat ttagcagcag - 3661 cacaaagcag atgtgtaaag tcactagatt tgggtgcttg cccacaatta gctcaactag - 3721 ctatagtatt atgcacaagc aaagttgaga ggttgtatgg tactgctgat ggaatggtaa - 3781 actctccaac agcattcctt aaggtgaata aagcacacgt accagtacca cttggtggtg - 3841 atggctcaat gtctattatg gagcttgcaa cagctggttt tgggatggca gataagaata - 3901 ttttaaaaaa tgcattcata tcttataagc atactcgtag agatggtgat aggtacgtat - 3961 tgggtttatt taaatttttg atgtcattaa gtgaggatgt attccagcac gaccgattgg - 4021 gtgagtttag ttttgtaggt aaagttcaat ggaaagtgtt cactcctaaa gctgaatttg - 4081 aatttcatga tcaattttca cataattatt tattagagtg gacacgtcaa catcctgtgt - 4141 atgactatat tattcctaga aatagagata atttgcttgt ataccttgta agaaagttga - 4201 atgatcctag catcattaca gctatgacta tgcagtcacc attacaactt cgtttccgta - 4261 tgcaagcaaa gcaacatatg aaagtatgcc ggtatgaagg tgaatgggtc acattcaggg - 4321 aggtacttgc tgcagctgat agttttgcta cgagttacca acctactgaa agggacatgg - 4381 atctctttaa tacacttgta agttgtacat tttctaaaga gtatgcttgg aaagactttt - 4441 taaatgaagt aaggtgtgag gtcttaacaa caagacatgt acataggcct aaaattgcta - 4501 ggacattcac tgttagagaa aaggaccagg ctatacaaaa tccaataaat tcggtgattg - 4561 gctataagta tgctcttaca gtggatgaag tcagtgatgt tcttgatagt gcattcttcc - 4621 cagagtctct atctgcagac ttacaggtta tgaaagatgg agtttacaga gaattaggac - 4681 ttgatataag ttctcctgaa gtcctaaaac gcatagcacc actattatat aaggcaggaa - 4741 ggtcacgtgt tgttattgtg gaaggaaatg tagaagggac agctgagtca atctgtagtt - 4801 attggctcaa gacaatgtca ctgattaaaa caatcagagt aagacctaag aaggaggtac - 4861 tgaaagctat gtctttatat agtgttaaag aaaatattgg attgcaggat gatattgcag - 4921 caactcgact atgcatagaa atctggagat ggtgtaaggc aaatgaacag gatgttaaag - 4981 aatggctaac atctctgtac tttgaaaaac agacattgat ggattgggta gaaaggttta - 5041 gaaggaaagg agttgttcct attgatcctg aaatacaatg tattggccta ctcttatatg - 5101 atgtattagg ttataaaagt gtgttacaaa tgcaagcaaa ccgaagagcc tattcaggta - 5161 agcaatatga tgcatactgt gtgcaaacat ataacgagga aacaaaacta tatgaaggtg - 5221 accttcgtgt tacttttaat tttggtttag attgtgcaag gttagaagtt ttttgggata - 5281 aaaaagagta tatcttagag acatctatca cccaacgaca tgtgttgcgg ttactgatgg - 5341 aagaagtgtc acaagaatta attagatgtg gaatgagatt caaaacagag caagtcaatc - 5401 aaactcggag cttagtgtta ttcaaaacag aggctggttt tgaatggggt aagcctaatg - 5461 tgccatgtat tgtatataaa cactgtgtct tgagaactgg gcttcgtacg aaacagccaa - 5521 ttaataaaga gttcatgata aatgtacaaa gtgatggttt ccgtgcaata gcacagatgg - 5581 atattgagag tccacggttc ttgttagcac atgcatatca tacactgcgt gatattagat - 5641 atcaagcagt gcaggcagta gggaatgtat ggtttaaaac agaacagcac aaactattta - 5701 ttaacccaat tatatcatca gggcttttag aaaactttat gaaaggctta cctgctgcca - 5761 tacctcctgc tgcatattcc ctcataatga acaaggctaa gatttctgtg gatttgttta - 5821 tgttcaatga gctattagca cttataaata ggaataatat cctcaacctt gatgggattg - 5881 aagaaacatc tgaaggttat agtactgtga catcaatgtc tagcaagcag tggtctgaag - 5941 agatgagttt aatgtctgat gatgatattg atgatatgga ggactttact atagcactgg - 6001 atgatattga ctttgaacaa ataaatttgg aagaggatat acaacacttt ctgcaggatg - 6061 aatcagcata tgttggtgat ttattgattc agacagaaga cattgaggtt aaaaagatac - 6121 gtggggtgac aagagtatta gagccagtca agctattaaa aagctgggtt tctaaaggcc - 6181 ttgctataga caaagtatac aatcctatcg ggataatctt aatggcaaga tacatgtcaa - 6241 aaacatacaa tttcagttca acacctcttg cactattaaa tccatatgac ttgacagaac - 6301 ttgaaagtgt tgtaaaggga tggggagaaa ctgtaaatga tcgattcaaa gatttagata - 6361 ttgaggcaca aacagttgtt aaagaaaagg gtgtacagcc agaagatgta ctccctgatt - 6421 cattattctc tttcaggcat gttgatgttt tgctgcgaag gttgttcccg cgtgaccctg - 6481 tatcaacatt ctattagtgg attttatacc ttattcatac agtatgtata ttgtagtgtt - 6541 cttttcccgg agcatactac ta -// diff --git a/andv/nextclade/L/sequences.fasta b/andv/nextclade/L/sequences.fasta deleted file mode 100644 index 30c0f8f..0000000 --- a/andv/nextclade/L/sequences.fasta +++ /dev/null @@ -1,111 +0,0 @@ ->NC_003468.2 Andes virus segment L, complete genome -TAGTAGTAGACTCCGGGATAGAAAAAGTTAGAAAAATGGAAAAGTATAGAGAGATTCATC -AGAGAGTTAGGGACCTTGCACCTGGAACGGTATCAGCATTAGAATGCATAGATCTACTGG -ATAGGCTCTACGCTGTCAGACATGACCTGGTTGACCAGATGATAAAACATGACTGGTCTG -ATAATAAAGATGTAGAAAGACCTATAGGTCAAGTTTTACTGATGGCTGGCATACCTAATG -ATATTATACAAGGCATGGAGAAGAAGATTATACCAAATAGCCCTTCTGGACAAGTATTGA -AAAGCTTTTTCCGAATGACACCAGATAATTATAAAATTACAGGTAACTTGATTGAGTTTA -TTGAAGTGACTGTAACAGCTGATGTGTCACGAGGTATTAGGGAGAAGAAAATAAAGTATG -AAGGAGGCCTCCAATTTGTTGAGCACTTACTGGAAACTGAATCAAGGAAGGGTAATATAC -CGCAACCTTATAAAATAACATTCTCAGTGGTTGCAGTTAAAACAGATGGATCAAACATCT -CGACTCAGTGGCCCAGTCGGAGGAACGATGGGGTAGTTCAGCACATGCGTCTAGTCCAAG -CTGATATAAATTATGTCAGAGAGCATTTAATAAAGTTAGATGAGAGAGCATCTTTGGAGG -CAATGTTTAACTTAAAGTTCCATGTATCAGGCCCTAAACTGAGATACTTTAACATCCCTG -ATTATAGACCACAGCAGCTATGTGAACCACGGATTGACAACTTAATACAATATTGCAAGA -ATTGGTTGACAAAAGAACATAAGTTTGTATTCAAAGAAGTCAGTGGAGCTAATGTGATTC -AAGCATTTGAGAGTCATGAACAGTTACATTTACAGAAATACAACGAATCACGAAAACCAA -GAAATTTTTTACTCTTGCAGCTTACAGTGCAAGGGGCATATCTACCATCAACAATCAGTT -CTGACCAGTGCAATACTAGGATTGGGTGTCTAGAAATATCAAAAAACCAACCAGAAACAC -CAGTACAGATGCTTGCATTGGATATATCTTATAAGTATCTGAGTCTTACAAGGGATGAGT -TGATCAATTATTATAGCCCTAGAGTGCACTTTCAATCGAGCCCTAATGTGAAGGAACCAG -GGACACTGAAGTTAGGATTATCACAATTAAATCCACTCTCTAAATCAATTCTTGACAATG -TTGGAAAGCATAAAAAGGATAAAGGATTATTTGGTGAGATCATAGATAGCATAAATGTGG -CAAGTCAAATACAGATCAATGCATGTGCAAAAATAATTGAGCAGATCTTATCAAATCTTG -AAATAAACATTGGAGAAATAAATGCTAGTATGCCTTCTCCTAATAAGACAACAGGTGTAG -ATGACCTGTTAAATAAATTTTATGATAATGAGCTTGGTAAATATATGTTATCCATTCTGA -GGAAAACAGCAGCATGGCATATAGGCCATCTAGTCAGAGATATCACAGAAAGTTTAATTG -CACATGCTGGGCTGCGCCGTTCTAAATATTGGTCAGTACATGCATATGACCATGGGAATG -TAATTTTGTTTATCTTGCCATCAAAGTCACTAGAGGTAGTAGGTTCTTATATAAGGTATT -TCACAGTATTTAAAGATGGTATAGGGTTGATAGACGCAGATAATATTGATTCTAAGGCCG -AAATTGATGGTGTCACCTGGTGTTATTCTAAGGTCATGAGTATTGATTTAAACAGGTTAT -TGGCTTTGAACATAGCTTTTGAGAAGTCACTTCTTGCCACGGCTACATGGTTCCAATATT -ATACTGAAGACCAAGGCCATTTTCCCCTTCAACATGCATTAAGGTCAATCTTTTCTTTCC -ACTTTTTACTCTGTGTGTCACAAAAGATGAAGCTATGTGCAATATTTGATAACCTTCGTT -ATCTGATACCATCAGTAACATCTTTGTACTCTGGGTACGAGTTGTTAATAGAAAAATTCT -TTGAGAGACCATTTAAGAGTTCACTGGATGTATACCTTTATTCTATCATAAAATCTCTAT -TAATTAGTTTGGCACAAAATAATAAAGTTCGATTTTACTCAAGAGTTCGTTTGTTAGGAT -TGACAGTTGATCACTCCACGGTCGGAGCAAGTGGTGTTTACCCCTCTTTAATGTCCCGTG -TTGTTTACAAACATTACAGAAGTTTAATCTCTGAAGCTACAACTTGTTTTTTCTTATTTG -AAAAGGGTTTGCATGGGAATTTACCAGAAGAGGCTAAAATACATCTTGAAACCATTGAAT -GGGCTCGGAAGTTCCAGGAGAAAGAAAAACAATATGGTGATATTCTTCTAAAGGAAGGCT -ATACAATTGAATCTGTAATCAATGGAGAAGTTGATGTAGAACAACAGCTTTTTTGTCAGG -AGGTCTCAGAGCTAAGTGCACAAGAGCTCAACAAATATTTACAGGCAAAATCTCAAGTTT -TATGTGCTAATATCATGAATAAACACTGGGACAAACCATATTTCAGTCAAACACGCAATA -TCAGTCTCAAGGGAATGTCTGGGGCATTGCAAGAGGATGGACATTTAGCTGCTAGTGTGA -CACTGATTGAAGCAATTAGGTTTTTAAATAGATCACAAACCAATCCAAATGTTATTGATA -TGTATGAGCAGACTAAACAATCAAAGGCACAAGCTAGGATTGTTAGGAAATACCAGAGAA -CAGAAGCAGATAGAGGATTTTTTATCACAACATTACCAACTAGGGTGCGATTAGAAATAA -TAGAAGATTATTTCGATGCAATTGCAAAGGTTGTGCCTGAAGAATATATTTCTTATGGTG -GGGATAAAAAAGTTCTAAATATTCAGAATGCACTAGAGAAAGCACTTAGATGGGCATCTG -GAGTATCAGAAATTACAACAAGCACTGGTAAAAGCATCAAGTTTAAGCGGAAATTAATGT -ATGTTAGTGCTGATGCCACAAAATGGTCACCAGGAGATAATTCTGCTAAGTTTAGGAGAT -TTACACAAGCAATATATGATGGCTTATCAGACAACAAACTGAAATGTTGTGTTGTTGATG -CATTACGTAACATTTATGAGACTGAATTTTTTATGTCCAGGAAATTACACCGATATATTG -ATAGTATGGAAAATCATTCAGATGCGGTTGAAGATTTCTTGGCATTTTTCTCAAATGGAG -TCTCAGCCAATGTAAAGGGAAACTGGCTTCAAGGGAACTTAAATAAATGCTCATCATTAT -TTGGTGCTGCTGTCTCATTACTTTTTCGGGAGGTCTGGAAACAATTGTTTCCAGAATTAG -AGTGTTTTTTTGAATTTGCACATCATTCAGATGATGCATTGTTCATTTATGGCTATCTGG -AGCCTGAAGATGATGGAACAGATTGGTTTTTGTATGTATCACAGCAGATACAGGCAGGAA -ACTTTCATTGGCATGCTATAAATCAAGAGATGTGGAAGAGCATGTTTAATCTACATGAGC -ACTTACTATTAATGGGTTCTATTAAAGTGTCACCTAAGAAGACAACAGTATCACCTACTA -ATGCAGAATTTCTTTCTACTTTTTTTGAAGGTTGTGCTGTGTCAATCCCTTTTGTTAAAA -TCTTACTGGGTTCATTATCAGATCTTCCTGGGTTAGGTTTCTTTGATGATTTAGCAGCAG -CACAAAGCAGATGTGTAAAGTCACTAGATTTGGGTGCTTGCCCACAATTAGCTCAACTAG -CTATAGTATTATGCACAAGCAAAGTTGAGAGGTTGTATGGTACTGCTGATGGAATGGTAA -ACTCTCCAACAGCATTCCTTAAGGTGAATAAAGCACACGTACCAGTACCACTTGGTGGTG -ATGGCTCAATGTCTATTATGGAGCTTGCAACAGCTGGTTTTGGGATGGCAGATAAGAATA -TTTTAAAAAATGCATTCATATCTTATAAGCATACTCGTAGAGATGGTGATAGGTACGTAT -TGGGTTTATTTAAATTTTTGATGTCATTAAGTGAGGATGTATTCCAGCACGACCGATTGG -GTGAGTTTAGTTTTGTAGGTAAAGTTCAATGGAAAGTGTTCACTCCTAAAGCTGAATTTG -AATTTCATGATCAATTTTCACATAATTATTTATTAGAGTGGACACGTCAACATCCTGTGT -ATGACTATATTATTCCTAGAAATAGAGATAATTTGCTTGTATACCTTGTAAGAAAGTTGA -ATGATCCTAGCATCATTACAGCTATGACTATGCAGTCACCATTACAACTTCGTTTCCGTA -TGCAAGCAAAGCAACATATGAAAGTATGCCGGTATGAAGGTGAATGGGTCACATTCAGGG -AGGTACTTGCTGCAGCTGATAGTTTTGCTACGAGTTACCAACCTACTGAAAGGGACATGG -ATCTCTTTAATACACTTGTAAGTTGTACATTTTCTAAAGAGTATGCTTGGAAAGACTTTT -TAAATGAAGTAAGGTGTGAGGTCTTAACAACAAGACATGTACATAGGCCTAAAATTGCTA -GGACATTCACTGTTAGAGAAAAGGACCAGGCTATACAAAATCCAATAAATTCGGTGATTG -GCTATAAGTATGCTCTTACAGTGGATGAAGTCAGTGATGTTCTTGATAGTGCATTCTTCC -CAGAGTCTCTATCTGCAGACTTACAGGTTATGAAAGATGGAGTTTACAGAGAATTAGGAC -TTGATATAAGTTCTCCTGAAGTCCTAAAACGCATAGCACCACTATTATATAAGGCAGGAA -GGTCACGTGTTGTTATTGTGGAAGGAAATGTAGAAGGGACAGCTGAGTCAATCTGTAGTT -ATTGGCTCAAGACAATGTCACTGATTAAAACAATCAGAGTAAGACCTAAGAAGGAGGTAC -TGAAAGCTATGTCTTTATATAGTGTTAAAGAAAATATTGGATTGCAGGATGATATTGCAG -CAACTCGACTATGCATAGAAATCTGGAGATGGTGTAAGGCAAATGAACAGGATGTTAAAG -AATGGCTAACATCTCTGTACTTTGAAAAACAGACATTGATGGATTGGGTAGAAAGGTTTA -GAAGGAAAGGAGTTGTTCCTATTGATCCTGAAATACAATGTATTGGCCTACTCTTATATG -ATGTATTAGGTTATAAAAGTGTGTTACAAATGCAAGCAAACCGAAGAGCCTATTCAGGTA -AGCAATATGATGCATACTGTGTGCAAACATATAACGAGGAAACAAAACTATATGAAGGTG -ACCTTCGTGTTACTTTTAATTTTGGTTTAGATTGTGCAAGGTTAGAAGTTTTTTGGGATA -AAAAAGAGTATATCTTAGAGACATCTATCACCCAACGACATGTGTTGCGGTTACTGATGG -AAGAAGTGTCACAAGAATTAATTAGATGTGGAATGAGATTCAAAACAGAGCAAGTCAATC -AAACTCGGAGCTTAGTGTTATTCAAAACAGAGGCTGGTTTTGAATGGGGTAAGCCTAATG -TGCCATGTATTGTATATAAACACTGTGTCTTGAGAACTGGGCTTCGTACGAAACAGCCAA -TTAATAAAGAGTTCATGATAAATGTACAAAGTGATGGTTTCCGTGCAATAGCACAGATGG -ATATTGAGAGTCCACGGTTCTTGTTAGCACATGCATATCATACACTGCGTGATATTAGAT -ATCAAGCAGTGCAGGCAGTAGGGAATGTATGGTTTAAAACAGAACAGCACAAACTATTTA -TTAACCCAATTATATCATCAGGGCTTTTAGAAAACTTTATGAAAGGCTTACCTGCTGCCA -TACCTCCTGCTGCATATTCCCTCATAATGAACAAGGCTAAGATTTCTGTGGATTTGTTTA -TGTTCAATGAGCTATTAGCACTTATAAATAGGAATAATATCCTCAACCTTGATGGGATTG -AAGAAACATCTGAAGGTTATAGTACTGTGACATCAATGTCTAGCAAGCAGTGGTCTGAAG -AGATGAGTTTAATGTCTGATGATGATATTGATGATATGGAGGACTTTACTATAGCACTGG -ATGATATTGACTTTGAACAAATAAATTTGGAAGAGGATATACAACACTTTCTGCAGGATG -AATCAGCATATGTTGGTGATTTATTGATTCAGACAGAAGACATTGAGGTTAAAAAGATAC -GTGGGGTGACAAGAGTATTAGAGCCAGTCAAGCTATTAAAAAGCTGGGTTTCTAAAGGCC -TTGCTATAGACAAAGTATACAATCCTATCGGGATAATCTTAATGGCAAGATACATGTCAA -AAACATACAATTTCAGTTCAACACCTCTTGCACTATTAAATCCATATGACTTGACAGAAC -TTGAAAGTGTTGTAAAGGGATGGGGAGAAACTGTAAATGATCGATTCAAAGATTTAGATA -TTGAGGCACAAACAGTTGTTAAAGAAAAGGGTGTACAGCCAGAAGATGTACTCCCTGATT -CATTATTCTCTTTCAGGCATGTTGATGTTTTGCTGCGAAGGTTGTTCCCGCGTGACCCTG -TATCAACATTCTATTAGTGGATTTTATACCTTATTCATACAGTATGTATATTGTAGTGTT -CTTTTCCCGGAGCATACTACTA diff --git a/andv/nextclade/M/CHANGELOG.md b/andv/nextclade/M/CHANGELOG.md deleted file mode 100644 index 0f72c1e..0000000 --- a/andv/nextclade/M/CHANGELOG.md +++ /dev/null @@ -1,5 +0,0 @@ -# Changelog - -## 2026-05-08 - -Initial minimal dataset generated from NCBI GenBank reference annotation. diff --git a/andv/nextclade/M/README.md b/andv/nextclade/M/README.md deleted file mode 100644 index 36d518e..0000000 --- a/andv/nextclade/M/README.md +++ /dev/null @@ -1,3 +0,0 @@ -# Andes virus M segment - -Minimal Nextclade dataset for Andes virus M segment using Andes virus reference. diff --git a/andv/nextclade/M/genome_annotation.gff3 b/andv/nextclade/M/genome_annotation.gff3 deleted file mode 100644 index 63806f7..0000000 --- a/andv/nextclade/M/genome_annotation.gff3 +++ /dev/null @@ -1,7 +0,0 @@ -##gff-version 3 -#!gff-spec-version 1.21 -#!processor NCBI annotwriter -##sequence-region NC_003467.2 1 3671 -##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1980456 -NC_003467.2 RefSeq region 1 3671 . + . ID=NC_003467.2:1..3671;Dbxref=taxon:1980456;Name=M;gbkey=Src;genome=genomic;mol_type=genomic RNA;old-name=Andes virus;segment=M;strain=Chile-9717869 -NC_003467.2 RefSeq CDS 52 3468 . + 0 Name=GPC;gbkey=CDS;locus_tag=ANDVsMgp1;protein_id=NP_604472.1;ID=cds-NP_604472.1;Dbxref=GenBank:NP_604472.1,GeneID:991233;product=G1 and G2 surface glycoprotein precursor diff --git a/andv/nextclade/M/pathogen.json b/andv/nextclade/M/pathogen.json deleted file mode 100644 index 5d5c6d1..0000000 --- a/andv/nextclade/M/pathogen.json +++ /dev/null @@ -1,39 +0,0 @@ -{ - "$schema": "https://raw.githubusercontent.com/nextstrain/nextclade/refs/heads/release/packages/nextclade-schemas/input-pathogen-json.schema.json", - "schemaVersion": "3.0.0", - "files": { - "reference": "reference.fasta", - "pathogenJson": "pathogen.json", - "genomeAnnotation": "genome_annotation.gff3", - "examples": "sequences.fasta", - "readme": "README.md", - "changelog": "CHANGELOG.md" - }, - "attributes": { - "name": "Andes virus M", - "reference name": "Andes virus segment M", - "reference accession": "NC_003467.2" - }, - "qc": { - "missingData": { - "enabled": true, - "missingDataThreshold": 2000, - "scoreBias": 500 - }, - "snpClusters": { - "enabled": false - }, - "mixedSites": { - "enabled": true, - "mixedSitesThreshold": 15 - }, - "frameShifts": { - "enabled": true, - "scoreWeight": 20 - }, - "stopCodons": { - "enabled": true, - "scoreWeight": 50 - } - } -} diff --git a/andv/nextclade/M/reference.fasta b/andv/nextclade/M/reference.fasta deleted file mode 100644 index 57fb40b..0000000 --- a/andv/nextclade/M/reference.fasta +++ /dev/null @@ -1,63 +0,0 @@ ->NC_003467.2 Andes virus segment M, complete genome -TAGTAGTAGACTCCGCAAGAAGAAGCAAAAAATTAAAGAAGTGAGTTTAAAATGGAAGGG -TGGTATCTGGTTGTTCTTGGAGTCTGCTATACGCTGACACTGGCAATGCCCAAGACCATT -TATGAGCTTAAAATGGAATGCCCGCACACTGTGGGTCTCGGTCAAGGTTACATCATTGGC -TCAACAGAACTAGGTTTGATCTCAATTGAGGCTGCATCTGATATAAAGCTCGAGAGCTCT -TGCAATTTTGATCTTCATACAACATCTATGGCCCAGAAGAGTTTCACCCAAGTTGAATGG -AGAAAGAAAAGTGACACAACTGATACCACAAATGCTGCGTCCACTACCTTTGAAGCACAA -ACTAAAACTGTTAACCTTAGAGGGACTTGTATACTGGCACCTGAACTCTATGATACATTG -AAGAAAGTAAAAAAGACAGTCCTGTGCTATGATCTAACATGTAATCAAACACATTGTCAG -CCAACTGTCTATCTGATTGCACCTGTATTGACATGCATGTCAATAAGAAGTTGTATGGCT -AGTGTGTTTACAAGCAGGATTCAGGTGATTTATGAAAAGACACATTGTGTAACAGGTCAG -CTGATTGAGGGTCAGTGTTTCAACCCAGCACACACATTGACATTATCTCAGCCTGCTCAC -ACTTATGATACTGTCACCCTTCCTATCTCTTGTTTTTTCACACCAAAGAAGTCGGAGCAA -CTAAAAGTTATAAAAACATTTGAAGGAATTCTGACGAAGACAGGTTGCACGGAGAATGCA -TTGCAGGGTTATTATGTGTGTTTTTTAGGGAGTCATTCAGAACCTTTAATTGTTCCGAGT -TTGGAGGACATACGGTCTGCTGAAGTTGTTAGTAGGATGCTTGTACACCCTAGGGGAGAA -GACCATGATGCCATACAGAATTCACAAAGTCACTTAAGAATAGTGGGACCTATCACAGCA -AAAGTGCCATCAACTAGTTCCACAGATACCCTAAAGGGGACAGCCTTTGCAGGCGTCCCA -ATGTATAGCTCTTTATCTACACTAGTCAGAAATGCAGACCCAGAATTTGTATTTTCTCCA -GGTATAGTACCTGAATCTAATCACAGTACATGTGATAAGAAGACAGTACCTATCACATGG -ACAGGCTACCTACCAATATCAGGTGAGATGGAAAAAGTGACTGGATGTACAGTTTTTTGT -ACACTAGCAGGACCTGGTGCTAGTTGTGAGGCCTATTCTGAAAATGGTATATTTAACATC -AGTTCTCCAACATGTCTTGTAAACAAAGTCCAAAGATTTCGTGGATCTGAACAGAAAATA -AATTTTATCTGTCAGCGGGTAGATCAGGATGTTGTTGTATACTGCAATGGGCAAAAGAAA -GTCATATTAACCAAAACTTTGGTTATTGGGCAGTGTATTTATACATTCACAAGCCTATTT -TCATTGATGCCTGATGTAGCCCACTCATTGGCTGTAGAATTATGTGTCCCGGGATTACAT -GGATGGGCCACTGTCATGCTTCTATCAACATTCTGCTTTGGGTGGGTCTTGATTCCTGCG -GTCACATTAATAATATTAAAGTGTCTAAGGGTTTTGACGTTTTCTTGTTCCCATTACACT -AATGAGTCAAAATTTAAATTCATCCTGGAAAAAGTTAAAATTGAATACCAAAAGACTATG -GGATCAATGGTGTGCGATGTATGTCATCATGAGTGTGAAACAGCAAAAGAACTTGAATCA -CATAGACAGAGTTGTATCAATGGACAATGTCCTTATTGCATGACAATAACTGAAGCAACT -GAAAGTGCCTTGCAAGCCCATTATTCCATTTGTAAATTGACAGGAAGATTTCAGGAGGCA -CTGAAAAAGTCACTTAAAAAGCCAGAGGTAAAAAAAGGTTGTTACAGAACACTCGGGGTA -TTTAGATATAAAAGTAGATGTTATGTGGGTTTGGTATGGTGCCTATTGTTGACATGTGAA -ATTGTTATTTGGGCCGCAAGTGCAGAGACTCCACTAATGGAGTCAGGCTGGTCAGATACG -GCTCATGGTGTTGGTGAGATTCCAATGAAGACAGACCTCGAGCTGGACTTTTCACTGCCT -TCTTCATCCTCTTACAGTTATAGGAGAAAGCTCACAAACCCAGCCAATAAAGAAGAGTCT -ATTCCCTTCCACTTCCAGATGGAAAAACAAGTAATTCATGCTGAAATCCAACCCCTGGGT -CATTGGATGGATGCGACATTTAATATTAAGACTGCATTTCATTGTTATGGTGCATGCCAG -AAATACTCTTATCCATGGCAGACATCTAAGTGCTTCTTTGAAAAGGACTACCAGTATGAA -ACAGGCTGGGGCTGTAATCCTGGTGACTGCCCAGGGGTTGGGACTGGATGCACTGCTTGT -GGTGTTTATCTCGATAAACTAAAATCTGTTGGGAAGGCCTATAAGATAATTTCTTTAAAA -TATACCAGAAAGGTTTGTATTCAGTTAGGAACAGAACAAACTTGCAAGCATATTGATGCA -AATGATTGTTTAGTGACACCATCTGTGAAAGTTTGCATAGTGGGCACAGTTTCAAAACTT -CAACCATCTGATACTCTTTTGTTCTTAGGTCCACTAGAACAAGGGGGAATCATTCTTAAG -CAATGGTGCACAACATCATGTGCATTTGGGGACCCTGGTGATATCATGTCCACTCCCAGT -GGTATGAGGTGTCCAGAGCACACTGGATCATTTAGGAAAATTTGCGGTTTTGCTACTACA -CCAGTTTGTGAATATCAAGGAAATACCATTTCTGGATATAAAAGAATGATGGCAACAAAA -GATTCATTCCAATCATTTAACTTAACAGAACCTCACATCACAACAAACAAGCTTGAATGG -ATCGACCCAGATGGGAATACAAGAGACCACGTAAACCTTGTCTTAAATAGAGATGTCTCA -TTTCAGGATTTAAGTGATAACCCCTGTAAAGTAGACCTACACACACAAGCAATAGAAGGG -GCATGGGGTTCTGGTGTAGGGTTTACACTCACATGTACTGTCGGATTAACAGAGTGCCCA -AGTTTTATGACATCAATTAAGGCATGTGACCTAGCTATGTGTTATGGATCAACAGTAACA -AACCTTGCCAGGGGCTCTAATACAGTGAAAGTAGTTGGTAAAGGAGGCCATTCAGGGTCC -TCATTTAAATGCTGTCATGATACAGATTGCTCCTCTGAAGGTTTACTTGCATCAGCCCCT -CATCTTGAGAGGGTAACAGGATTCAATCAAATTGATTCAGATAAGGTTTATGATGATGGT -GCACCACCTTGCACATTCAAATGCTGGTTCACTAAGTCAGGTGAGTGGCTTCTTGGGATC -TTAAACGGGAATTGGATTGTTGTTGTAGTGCTTGTTGTGATACTCATTCTCTCTATCATA -ATGTTCAGTGTTTTGTGTCCCAGGAGAGGGCACAAGAAAACTGTCTAAGCATTGACCTCA -ACTCCTACATTAGATCATATACATTTATGCACTTCCTCATATTTAGCTGCACTAAGATAT -TAATAAACTCTAGTTATTGACTTTATAAGATTATTATGGAACTAACCTCACTTAAAAAAA -ACAAATACTTTACTCATATATAACTCCATATTCTCTTACCGAGGCTTTTGTTCCTGCGGA -GCATACTACTA diff --git a/andv/nextclade/M/reference.gb b/andv/nextclade/M/reference.gb deleted file mode 100644 index afb076d..0000000 --- a/andv/nextclade/M/reference.gb +++ /dev/null @@ -1,119 +0,0 @@ -LOCUS NC_003467 3671 bp RNA linear VRL 13-AUG-2018 -DEFINITION Andes virus segment M, complete genome. -ACCESSION NC_003467 -VERSION NC_003467.2 -DBLINK BioProject: PRJNA485481 -KEYWORDS RefSeq. -SOURCE Orthohantavirus andesense - ORGANISM Orthohantavirus andesense - Viruses; Riboviria; Orthornavirae; Negarnaviricota; - Polyploviricotina; Bunyaviricetes; Elliovirales; Hantaviridae; - Mammantavirinae; Orthohantavirus. -REFERENCE 1 (bases 1 to 3671) - AUTHORS Meissner,J.D., Rowe,J.E., Borucki,M.K. and St Jeor,S.C. - TITLE Complete nucleotide sequence of a Chilean hantavirus - JOURNAL Virus Res. 89 (1), 131-143 (2002) - PUBMED 12367756 -REFERENCE 2 (bases 1 to 3671) - AUTHORS Meissner,J.D. and St. Jeor,S.C. - TITLE Hantavirus strain Andes 23 M segment sequence - JOURNAL Unpublished -REFERENCE 3 (bases 1 to 3671) - CONSRTM NCBI Genome Project - TITLE Direct Submission - JOURNAL Submitted (17-NOV-2010) National Center for Biotechnology - Information, NIH, Bethesda, MD 20894, USA -REFERENCE 4 (bases 1 to 3671) - AUTHORS Meissner,J.D. and St. Jeor,S.C. - TITLE Direct Submission - JOURNAL Submitted (02-OCT-2002) Microbiology, University of Nevada-Reno, - FA310/MS200, Reno, NV 89557, USA - REMARK Sequence update by submitter -REFERENCE 5 (bases 1 to 3671) - AUTHORS Meissner,J.D. and St. Jeor,S.C. - TITLE Direct Submission - JOURNAL Submitted (01-AUG-2000) Microbiology, University of Nevada-Reno, - FA310/MS200, Reno, NV 89557, USA -COMMENT PROVISIONAL REFSEQ: This record has not yet been subject to final - NCBI review. The reference sequence is identical to AF291703. - On Oct 2, 2002 this sequence version replaced NC_003467.1. - COMPLETENESS: full length. -FEATURES Location/Qualifiers - source 1..3671 - /organism="Orthohantavirus andesense" - /mol_type="genomic RNA" - /strain="Chile-9717869" - /db_xref="taxon:1980456" - /segment="M" - CDS 52..3468 - /ID="cds-NP_604472.1" - /Dbxref="GenBank:NP_604472.1,GeneID:991233" - /Name="GPC" - /gbkey="CDS" - /locus_tag="GPC" - /product="G1 and G2 surface glycoprotein precursor" - /protein_id="NP_604472.1" -ORIGIN - 1 tagtagtaga ctccgcaaga agaagcaaaa aattaaagaa gtgagtttaa aatggaaggg - 61 tggtatctgg ttgttcttgg agtctgctat acgctgacac tggcaatgcc caagaccatt - 121 tatgagctta aaatggaatg cccgcacact gtgggtctcg gtcaaggtta catcattggc - 181 tcaacagaac taggtttgat ctcaattgag gctgcatctg atataaagct cgagagctct - 241 tgcaattttg atcttcatac aacatctatg gcccagaaga gtttcaccca agttgaatgg - 301 agaaagaaaa gtgacacaac tgataccaca aatgctgcgt ccactacctt tgaagcacaa - 361 actaaaactg ttaaccttag agggacttgt atactggcac ctgaactcta tgatacattg - 421 aagaaagtaa aaaagacagt cctgtgctat gatctaacat gtaatcaaac acattgtcag - 481 ccaactgtct atctgattgc acctgtattg acatgcatgt caataagaag ttgtatggct - 541 agtgtgttta caagcaggat tcaggtgatt tatgaaaaga cacattgtgt aacaggtcag - 601 ctgattgagg gtcagtgttt caacccagca cacacattga cattatctca gcctgctcac - 661 acttatgata ctgtcaccct tcctatctct tgttttttca caccaaagaa gtcggagcaa - 721 ctaaaagtta taaaaacatt tgaaggaatt ctgacgaaga caggttgcac ggagaatgca - 781 ttgcagggtt attatgtgtg ttttttaggg agtcattcag aacctttaat tgttccgagt - 841 ttggaggaca tacggtctgc tgaagttgtt agtaggatgc ttgtacaccc taggggagaa - 901 gaccatgatg ccatacagaa ttcacaaagt cacttaagaa tagtgggacc tatcacagca - 961 aaagtgccat caactagttc cacagatacc ctaaagggga cagcctttgc aggcgtccca - 1021 atgtatagct ctttatctac actagtcaga aatgcagacc cagaatttgt attttctcca - 1081 ggtatagtac ctgaatctaa tcacagtaca tgtgataaga agacagtacc tatcacatgg - 1141 acaggctacc taccaatatc aggtgagatg gaaaaagtga ctggatgtac agttttttgt - 1201 acactagcag gacctggtgc tagttgtgag gcctattctg aaaatggtat atttaacatc - 1261 agttctccaa catgtcttgt aaacaaagtc caaagatttc gtggatctga acagaaaata - 1321 aattttatct gtcagcgggt agatcaggat gttgttgtat actgcaatgg gcaaaagaaa - 1381 gtcatattaa ccaaaacttt ggttattggg cagtgtattt atacattcac aagcctattt - 1441 tcattgatgc ctgatgtagc ccactcattg gctgtagaat tatgtgtccc gggattacat - 1501 ggatgggcca ctgtcatgct tctatcaaca ttctgctttg ggtgggtctt gattcctgcg - 1561 gtcacattaa taatattaaa gtgtctaagg gttttgacgt tttcttgttc ccattacact - 1621 aatgagtcaa aatttaaatt catcctggaa aaagttaaaa ttgaatacca aaagactatg - 1681 ggatcaatgg tgtgcgatgt atgtcatcat gagtgtgaaa cagcaaaaga acttgaatca - 1741 catagacaga gttgtatcaa tggacaatgt ccttattgca tgacaataac tgaagcaact - 1801 gaaagtgcct tgcaagccca ttattccatt tgtaaattga caggaagatt tcaggaggca - 1861 ctgaaaaagt cacttaaaaa gccagaggta aaaaaaggtt gttacagaac actcggggta - 1921 tttagatata aaagtagatg ttatgtgggt ttggtatggt gcctattgtt gacatgtgaa - 1981 attgttattt gggccgcaag tgcagagact ccactaatgg agtcaggctg gtcagatacg - 2041 gctcatggtg ttggtgagat tccaatgaag acagacctcg agctggactt ttcactgcct - 2101 tcttcatcct cttacagtta taggagaaag ctcacaaacc cagccaataa agaagagtct - 2161 attcccttcc acttccagat ggaaaaacaa gtaattcatg ctgaaatcca acccctgggt - 2221 cattggatgg atgcgacatt taatattaag actgcatttc attgttatgg tgcatgccag - 2281 aaatactctt atccatggca gacatctaag tgcttctttg aaaaggacta ccagtatgaa - 2341 acaggctggg gctgtaatcc tggtgactgc ccaggggttg ggactggatg cactgcttgt - 2401 ggtgtttatc tcgataaact aaaatctgtt gggaaggcct ataagataat ttctttaaaa - 2461 tataccagaa aggtttgtat tcagttagga acagaacaaa cttgcaagca tattgatgca - 2521 aatgattgtt tagtgacacc atctgtgaaa gtttgcatag tgggcacagt ttcaaaactt - 2581 caaccatctg atactctttt gttcttaggt ccactagaac aagggggaat cattcttaag - 2641 caatggtgca caacatcatg tgcatttggg gaccctggtg atatcatgtc cactcccagt - 2701 ggtatgaggt gtccagagca cactggatca tttaggaaaa tttgcggttt tgctactaca - 2761 ccagtttgtg aatatcaagg aaataccatt tctggatata aaagaatgat ggcaacaaaa - 2821 gattcattcc aatcatttaa cttaacagaa cctcacatca caacaaacaa gcttgaatgg - 2881 atcgacccag atgggaatac aagagaccac gtaaaccttg tcttaaatag agatgtctca - 2941 tttcaggatt taagtgataa cccctgtaaa gtagacctac acacacaagc aatagaaggg - 3001 gcatggggtt ctggtgtagg gtttacactc acatgtactg tcggattaac agagtgccca - 3061 agttttatga catcaattaa ggcatgtgac ctagctatgt gttatggatc aacagtaaca - 3121 aaccttgcca ggggctctaa tacagtgaaa gtagttggta aaggaggcca ttcagggtcc - 3181 tcatttaaat gctgtcatga tacagattgc tcctctgaag gtttacttgc atcagcccct - 3241 catcttgaga gggtaacagg attcaatcaa attgattcag ataaggttta tgatgatggt - 3301 gcaccacctt gcacattcaa atgctggttc actaagtcag gtgagtggct tcttgggatc - 3361 ttaaacggga attggattgt tgttgtagtg cttgttgtga tactcattct ctctatcata - 3421 atgttcagtg ttttgtgtcc caggagaggg cacaagaaaa ctgtctaagc attgacctca - 3481 actcctacat tagatcatat acatttatgc acttcctcat atttagctgc actaagatat - 3541 taataaactc tagttattga ctttataaga ttattatgga actaacctca cttaaaaaaa - 3601 acaaatactt tactcatata taactccata ttctcttacc gaggcttttg ttcctgcgga - 3661 gcatactact a -// diff --git a/andv/nextclade/M/sequences.fasta b/andv/nextclade/M/sequences.fasta deleted file mode 100644 index 57fb40b..0000000 --- a/andv/nextclade/M/sequences.fasta +++ /dev/null @@ -1,63 +0,0 @@ ->NC_003467.2 Andes virus segment M, complete genome -TAGTAGTAGACTCCGCAAGAAGAAGCAAAAAATTAAAGAAGTGAGTTTAAAATGGAAGGG -TGGTATCTGGTTGTTCTTGGAGTCTGCTATACGCTGACACTGGCAATGCCCAAGACCATT -TATGAGCTTAAAATGGAATGCCCGCACACTGTGGGTCTCGGTCAAGGTTACATCATTGGC -TCAACAGAACTAGGTTTGATCTCAATTGAGGCTGCATCTGATATAAAGCTCGAGAGCTCT -TGCAATTTTGATCTTCATACAACATCTATGGCCCAGAAGAGTTTCACCCAAGTTGAATGG -AGAAAGAAAAGTGACACAACTGATACCACAAATGCTGCGTCCACTACCTTTGAAGCACAA -ACTAAAACTGTTAACCTTAGAGGGACTTGTATACTGGCACCTGAACTCTATGATACATTG -AAGAAAGTAAAAAAGACAGTCCTGTGCTATGATCTAACATGTAATCAAACACATTGTCAG -CCAACTGTCTATCTGATTGCACCTGTATTGACATGCATGTCAATAAGAAGTTGTATGGCT -AGTGTGTTTACAAGCAGGATTCAGGTGATTTATGAAAAGACACATTGTGTAACAGGTCAG -CTGATTGAGGGTCAGTGTTTCAACCCAGCACACACATTGACATTATCTCAGCCTGCTCAC -ACTTATGATACTGTCACCCTTCCTATCTCTTGTTTTTTCACACCAAAGAAGTCGGAGCAA -CTAAAAGTTATAAAAACATTTGAAGGAATTCTGACGAAGACAGGTTGCACGGAGAATGCA -TTGCAGGGTTATTATGTGTGTTTTTTAGGGAGTCATTCAGAACCTTTAATTGTTCCGAGT -TTGGAGGACATACGGTCTGCTGAAGTTGTTAGTAGGATGCTTGTACACCCTAGGGGAGAA -GACCATGATGCCATACAGAATTCACAAAGTCACTTAAGAATAGTGGGACCTATCACAGCA -AAAGTGCCATCAACTAGTTCCACAGATACCCTAAAGGGGACAGCCTTTGCAGGCGTCCCA -ATGTATAGCTCTTTATCTACACTAGTCAGAAATGCAGACCCAGAATTTGTATTTTCTCCA -GGTATAGTACCTGAATCTAATCACAGTACATGTGATAAGAAGACAGTACCTATCACATGG -ACAGGCTACCTACCAATATCAGGTGAGATGGAAAAAGTGACTGGATGTACAGTTTTTTGT -ACACTAGCAGGACCTGGTGCTAGTTGTGAGGCCTATTCTGAAAATGGTATATTTAACATC -AGTTCTCCAACATGTCTTGTAAACAAAGTCCAAAGATTTCGTGGATCTGAACAGAAAATA -AATTTTATCTGTCAGCGGGTAGATCAGGATGTTGTTGTATACTGCAATGGGCAAAAGAAA -GTCATATTAACCAAAACTTTGGTTATTGGGCAGTGTATTTATACATTCACAAGCCTATTT -TCATTGATGCCTGATGTAGCCCACTCATTGGCTGTAGAATTATGTGTCCCGGGATTACAT -GGATGGGCCACTGTCATGCTTCTATCAACATTCTGCTTTGGGTGGGTCTTGATTCCTGCG -GTCACATTAATAATATTAAAGTGTCTAAGGGTTTTGACGTTTTCTTGTTCCCATTACACT -AATGAGTCAAAATTTAAATTCATCCTGGAAAAAGTTAAAATTGAATACCAAAAGACTATG -GGATCAATGGTGTGCGATGTATGTCATCATGAGTGTGAAACAGCAAAAGAACTTGAATCA -CATAGACAGAGTTGTATCAATGGACAATGTCCTTATTGCATGACAATAACTGAAGCAACT -GAAAGTGCCTTGCAAGCCCATTATTCCATTTGTAAATTGACAGGAAGATTTCAGGAGGCA -CTGAAAAAGTCACTTAAAAAGCCAGAGGTAAAAAAAGGTTGTTACAGAACACTCGGGGTA -TTTAGATATAAAAGTAGATGTTATGTGGGTTTGGTATGGTGCCTATTGTTGACATGTGAA -ATTGTTATTTGGGCCGCAAGTGCAGAGACTCCACTAATGGAGTCAGGCTGGTCAGATACG -GCTCATGGTGTTGGTGAGATTCCAATGAAGACAGACCTCGAGCTGGACTTTTCACTGCCT -TCTTCATCCTCTTACAGTTATAGGAGAAAGCTCACAAACCCAGCCAATAAAGAAGAGTCT -ATTCCCTTCCACTTCCAGATGGAAAAACAAGTAATTCATGCTGAAATCCAACCCCTGGGT -CATTGGATGGATGCGACATTTAATATTAAGACTGCATTTCATTGTTATGGTGCATGCCAG -AAATACTCTTATCCATGGCAGACATCTAAGTGCTTCTTTGAAAAGGACTACCAGTATGAA -ACAGGCTGGGGCTGTAATCCTGGTGACTGCCCAGGGGTTGGGACTGGATGCACTGCTTGT -GGTGTTTATCTCGATAAACTAAAATCTGTTGGGAAGGCCTATAAGATAATTTCTTTAAAA -TATACCAGAAAGGTTTGTATTCAGTTAGGAACAGAACAAACTTGCAAGCATATTGATGCA -AATGATTGTTTAGTGACACCATCTGTGAAAGTTTGCATAGTGGGCACAGTTTCAAAACTT -CAACCATCTGATACTCTTTTGTTCTTAGGTCCACTAGAACAAGGGGGAATCATTCTTAAG -CAATGGTGCACAACATCATGTGCATTTGGGGACCCTGGTGATATCATGTCCACTCCCAGT -GGTATGAGGTGTCCAGAGCACACTGGATCATTTAGGAAAATTTGCGGTTTTGCTACTACA -CCAGTTTGTGAATATCAAGGAAATACCATTTCTGGATATAAAAGAATGATGGCAACAAAA -GATTCATTCCAATCATTTAACTTAACAGAACCTCACATCACAACAAACAAGCTTGAATGG -ATCGACCCAGATGGGAATACAAGAGACCACGTAAACCTTGTCTTAAATAGAGATGTCTCA -TTTCAGGATTTAAGTGATAACCCCTGTAAAGTAGACCTACACACACAAGCAATAGAAGGG -GCATGGGGTTCTGGTGTAGGGTTTACACTCACATGTACTGTCGGATTAACAGAGTGCCCA -AGTTTTATGACATCAATTAAGGCATGTGACCTAGCTATGTGTTATGGATCAACAGTAACA -AACCTTGCCAGGGGCTCTAATACAGTGAAAGTAGTTGGTAAAGGAGGCCATTCAGGGTCC -TCATTTAAATGCTGTCATGATACAGATTGCTCCTCTGAAGGTTTACTTGCATCAGCCCCT -CATCTTGAGAGGGTAACAGGATTCAATCAAATTGATTCAGATAAGGTTTATGATGATGGT -GCACCACCTTGCACATTCAAATGCTGGTTCACTAAGTCAGGTGAGTGGCTTCTTGGGATC -TTAAACGGGAATTGGATTGTTGTTGTAGTGCTTGTTGTGATACTCATTCTCTCTATCATA -ATGTTCAGTGTTTTGTGTCCCAGGAGAGGGCACAAGAAAACTGTCTAAGCATTGACCTCA -ACTCCTACATTAGATCATATACATTTATGCACTTCCTCATATTTAGCTGCACTAAGATAT -TAATAAACTCTAGTTATTGACTTTATAAGATTATTATGGAACTAACCTCACTTAAAAAAA -ACAAATACTTTACTCATATATAACTCCATATTCTCTTACCGAGGCTTTTGTTCCTGCGGA -GCATACTACTA diff --git a/andv/nextclade/S/CHANGELOG.md b/andv/nextclade/S/CHANGELOG.md deleted file mode 100644 index 0f72c1e..0000000 --- a/andv/nextclade/S/CHANGELOG.md +++ /dev/null @@ -1,5 +0,0 @@ -# Changelog - -## 2026-05-08 - -Initial minimal dataset generated from NCBI GenBank reference annotation. diff --git a/andv/nextclade/S/README.md b/andv/nextclade/S/README.md deleted file mode 100644 index 69ed153..0000000 --- a/andv/nextclade/S/README.md +++ /dev/null @@ -1,3 +0,0 @@ -# Andes virus S segment - -Minimal Nextclade dataset for Andes virus S segment using Andes virus reference. diff --git a/andv/nextclade/S/genome_annotation.gff3 b/andv/nextclade/S/genome_annotation.gff3 deleted file mode 100644 index 2f0415f..0000000 --- a/andv/nextclade/S/genome_annotation.gff3 +++ /dev/null @@ -1,8 +0,0 @@ -##gff-version 3 -#!gff-spec-version 1.21 -#!processor NCBI annotwriter -##sequence-region NC_003466.1 1 1871 -##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1980456 -NC_003466.1 RefSeq region 1 1871 . + . ID=NC_003466.1:1..1871;Dbxref=taxon:1980456;Name=S;gbkey=Src;genome=genomic;mol_type=viral cRNA;old-name=Andes virus;segment=S;strain=Chile-9717869 -NC_003466.1 RefSeq CDS 43 1329 . + 0 Name=N;gbkey=CDS;locus_tag=ANDVsSgp1;protein_id=NP_604471.1;ID=cds-NP_604471.1;product=nucleocapsid protein;Dbxref=GenBank:NP_604471.1,GeneID:991232 -NC_003466.1 RefSeq CDS 122 313 . + 0 Name=NSs;gbkey=CDS;locus_tag=ANDVsSgp2;protein_id=YP_004928151.1;ID=cds-YP_004928151.1;product=putative nonstructural protein;Dbxref=GenBank:YP_004928151.1,GeneID:11293630 diff --git a/andv/nextclade/S/pathogen.json b/andv/nextclade/S/pathogen.json deleted file mode 100644 index 37414f8..0000000 --- a/andv/nextclade/S/pathogen.json +++ /dev/null @@ -1,39 +0,0 @@ -{ - "$schema": "https://raw.githubusercontent.com/nextstrain/nextclade/refs/heads/release/packages/nextclade-schemas/input-pathogen-json.schema.json", - "schemaVersion": "3.0.0", - "files": { - "reference": "reference.fasta", - "pathogenJson": "pathogen.json", - "genomeAnnotation": "genome_annotation.gff3", - "examples": "sequences.fasta", - "readme": "README.md", - "changelog": "CHANGELOG.md" - }, - "attributes": { - "name": "Andes virus S", - "reference name": "Andes virus segment S", - "reference accession": "NC_003466.1" - }, - "qc": { - "missingData": { - "enabled": true, - "missingDataThreshold": 2000, - "scoreBias": 500 - }, - "snpClusters": { - "enabled": false - }, - "mixedSites": { - "enabled": true, - "mixedSitesThreshold": 15 - }, - "frameShifts": { - "enabled": true, - "scoreWeight": 20 - }, - "stopCodons": { - "enabled": true, - "scoreWeight": 50 - } - } -} diff --git a/andv/nextclade/S/reference.fasta b/andv/nextclade/S/reference.fasta deleted file mode 100644 index 5cdfd94..0000000 --- a/andv/nextclade/S/reference.fasta +++ /dev/null @@ -1,33 +0,0 @@ ->NC_003466.1 Andes virus segment S, complete sequence -TAGTAGTAGACTCCTTGAGAAGCTACTGCTGCGAAAGCTGGAATGAGCACCCTCCAAGAA -TTGCAGGAAAACATCACAGCACACGAACAACAGCTCGTGACTGCTCGGCAAAAGCTTAAG -GATGCCGAGAAGGCAGTGGAGGTGGACCCGGATGACGTTAACAAGAGCACACTACAAAGT -AGACGGGCAGCTGTGTCTACATTGGAGACCAAACTCGGAGAACTTAAGAGGCAACTTGCA -GATTTGGTGGCAGCTCAAAAATTGGCTACAAAACCAGTTGATCCAACAGGGCTTGAGCCT -GATGATCATCTAAAGGAAAAATCATCTCTGAGATATGGGAATGTCCTGGATGTTAATTCA -ATTGATTTGGAAGAACCGAGTGGACAGACTGCTGATTGGAAGGCTATAGGAGCATACATC -TTAGGGTTTGCAATTCCGATCATCCTAAAGGCCTTATACATGCTGTCAACCCGTGGGAGA -CAAACTGTGAAAGACAACAAAGGGACCAGGATAAGGTTTAAGGATGATTCTTCCTTTGAA -GAAGTCAATGGGATACGTAAACCAAAACACCTTTACGTCTCAATGCCAACTGCACAGTCC -ACTATGAAGGCTGAAGAAATCACGCCAGGACGATTTAGGACAATTGCTTGTGGCCTTTTT -CCAGCACAGGTCAAAGCCCGAAATATAATAAGTCCTGTAATGGGAGTAATTGGATTTGGC -TTCTTTGTAAAGGATTGGATGGATCGGATAGAAGAGTTTCTGGCTGCAGAGTGTCCATTC -TTACCTAAGCCAAAGGTCGCCTCAGAAGCCTTCATGTCTACCAATAAGATGTATTTTCTG -AACAGACAGAGACAAGTCAATGAATCTAAGGTTCAAGATATTATCGATTTGATAGACCAT -GCTGAGACCGAGTCTGCTACCTTGTTTACAGAGATTGCAACACCCCATTCAGTCTGGGTG -TTTGCATGTGCACCTGACCGGTGCCCTCCAACTGCATTGTATGTTGCAGGGGTACCGGAA -CTTGGTGCATTTTTTTCTATCCTTCAGGACATGCGTAATACCATCATGGCATCTAAATCT -GTAGGGACTGCAGAAGAGAAGCTAAAGAAAAAATCTGCCTTCTACCAATCATACCTAAGA -AGGACACAATCTATGGGAATCCAACTGGACCAGAAGATCATAATCCTTTACATGCTATCA -TGGGGTAAAGAAGCTGTGAATCACTTCCATCTTGGTGATGATATGGACCCTGAACTCAGG -CAGCTAGCACAATCTCTGATCGATACTAAGGTGAAGGAGATCTCCAACCAAGAGCCACTT -AAGTTGTAGGTGCTTAATGAAATCATGATTGAAGAAAGACTTTCCGGGCTTGTGCCACAT -ATTAATCATCTCAGGACCTATCCTTAATGTGATTAATAGGGTTTTATTATAAGGGCAGTT -AATGGGGTTGGTTACTAACTATGGGTAAGGGTTCATTACCATTTTTGCACTAGGGTTAAA -GGGCCACTACATTGTATTTGCACTAAGGGAAATGGGAGGTGGGTTAGTTTGTATTTAGTT -GTTAAGTTTTTTATAATCATATGTTAATGAGGAATTAGCTATATGATATCACTGATTGAT -TGGCTATTTTTAGGTTAAGTAATTGTAGTTAAATAGTTGTGTTAAGTTAGTATGTTAAGG -TTTATAGGTTAAGATTTACTAACAATCATATTATGTCATTAGATGTAAATTTCATTCCTG -GCTTGCTTCTGCTTTCGCATTGCTAACCTACAACAAGACTACCTCACCCACTACCCCTCC -CCTATTCTACCTCAACACATACTACCTCACATTTGATTTTTCTTGATTGCTTTTCAAGGA -GCATACTACTA diff --git a/andv/nextclade/S/reference.gb b/andv/nextclade/S/reference.gb deleted file mode 100644 index 29f5867..0000000 --- a/andv/nextclade/S/reference.gb +++ /dev/null @@ -1,97 +0,0 @@ -LOCUS NC_003466 1871 bp cRNA linear VRL 13-AUG-2018 -DEFINITION Andes virus segment S, complete sequence. -ACCESSION NC_003466 -VERSION NC_003466.1 -DBLINK BioProject: PRJNA485481 -KEYWORDS RefSeq. -SOURCE Orthohantavirus andesense - ORGANISM Orthohantavirus andesense - Viruses; Riboviria; Orthornavirae; Negarnaviricota; - Polyploviricotina; Bunyaviricetes; Elliovirales; Hantaviridae; - Mammantavirinae; Orthohantavirus. -REFERENCE 1 (bases 1 to 1871) - AUTHORS Meissner,J., Rowe,J., Borucki,M. and St Jeor,S. - TITLE Complete nucleotide sequence of a Chilean hantavirus - JOURNAL Virus Res. 89 (1), 131 (2002) - PUBMED 12367756 -REFERENCE 2 (bases 47 to 1475) - AUTHORS Bohlman,M.C., Morzunov,S.P., Meissner,J., Taylor,M.B., Ishibashi,K., - Rowe,J., Levis,S., Enria,D. and St Jeor,S.C. - TITLE Analysis of hantavirus genetic diversity in Argentina: S - segment-derived phylogeny - JOURNAL J. Virol. 76 (8), 3765-3773 (2002) - PUBMED 11907216 -REFERENCE 3 (bases 1 to 1871) - AUTHORS Meissner,J.D. and St. Jeor,S.C. - TITLE Hantavirus S segment nucleocapsid protein gene - JOURNAL Unpublished -REFERENCE 4 (bases 1 to 1871) - CONSRTM NCBI Genome Project - TITLE Direct Submission - JOURNAL Submitted (27-MAR-2002) National Center for Biotechnology - Information, NIH, Bethesda, MD 20894, USA -REFERENCE 5 (bases 1 to 1871) - AUTHORS Meissner,J.D. and St. Jeor,S.C. - TITLE Direct Submission - JOURNAL Submitted (01-AUG-2000) Microbiology, University of Nevada-Reno, - FA310/MS200, Reno, NV 89557, USA -COMMENT PROVISIONAL REFSEQ: This record has not yet been subject to final - NCBI review. The reference sequence was derived from AF291702. - COMPLETENESS: full length. -FEATURES Location/Qualifiers - source 1..1871 - /organism="Orthohantavirus andesense" - /mol_type="viral cRNA" - /strain="Chile-9717869" - /db_xref="taxon:1980456" - /segment="S" - CDS 43..1329 - /ID="cds-NP_604471.1" - /Dbxref="GenBank:NP_604471.1,GeneID:991232" - /Name="N" - /gbkey="CDS" - /locus_tag="N" - /product="nucleocapsid protein" - /protein_id="NP_604471.1" - CDS 122..313 - /ID="cds-YP_004928151.1" - /Dbxref="GenBank:YP_004928151.1,GeneID:11293630" - /Name="NSs" - /gbkey="CDS" - /locus_tag="NSs" - /product="putative nonstructural protein" - /protein_id="YP_004928151.1" -ORIGIN - 1 tagtagtaga ctccttgaga agctactgct gcgaaagctg gaatgagcac cctccaagaa - 61 ttgcaggaaa acatcacagc acacgaacaa cagctcgtga ctgctcggca aaagcttaag - 121 gatgccgaga aggcagtgga ggtggacccg gatgacgtta acaagagcac actacaaagt - 181 agacgggcag ctgtgtctac attggagacc aaactcggag aacttaagag gcaacttgca - 241 gatttggtgg cagctcaaaa attggctaca aaaccagttg atccaacagg gcttgagcct - 301 gatgatcatc taaaggaaaa atcatctctg agatatggga atgtcctgga tgttaattca - 361 attgatttgg aagaaccgag tggacagact gctgattgga aggctatagg agcatacatc - 421 ttagggtttg caattccgat catcctaaag gccttataca tgctgtcaac ccgtgggaga - 481 caaactgtga aagacaacaa agggaccagg ataaggttta aggatgattc ttcctttgaa - 541 gaagtcaatg ggatacgtaa accaaaacac ctttacgtct caatgccaac tgcacagtcc - 601 actatgaagg ctgaagaaat cacgccagga cgatttagga caattgcttg tggccttttt - 661 ccagcacagg tcaaagcccg aaatataata agtcctgtaa tgggagtaat tggatttggc - 721 ttctttgtaa aggattggat ggatcggata gaagagtttc tggctgcaga gtgtccattc - 781 ttacctaagc caaaggtcgc ctcagaagcc ttcatgtcta ccaataagat gtattttctg - 841 aacagacaga gacaagtcaa tgaatctaag gttcaagata ttatcgattt gatagaccat - 901 gctgagaccg agtctgctac cttgtttaca gagattgcaa caccccattc agtctgggtg - 961 tttgcatgtg cacctgaccg gtgccctcca actgcattgt atgttgcagg ggtaccggaa - 1021 cttggtgcat ttttttctat ccttcaggac atgcgtaata ccatcatggc atctaaatct - 1081 gtagggactg cagaagagaa gctaaagaaa aaatctgcct tctaccaatc atacctaaga - 1141 aggacacaat ctatgggaat ccaactggac cagaagatca taatccttta catgctatca - 1201 tggggtaaag aagctgtgaa tcacttccat cttggtgatg atatggaccc tgaactcagg - 1261 cagctagcac aatctctgat cgatactaag gtgaaggaga tctccaacca agagccactt - 1321 aagttgtagg tgcttaatga aatcatgatt gaagaaagac tttccgggct tgtgccacat - 1381 attaatcatc tcaggaccta tccttaatgt gattaatagg gttttattat aagggcagtt - 1441 aatggggttg gttactaact atgggtaagg gttcattacc atttttgcac tagggttaaa - 1501 gggccactac attgtatttg cactaaggga aatgggaggt gggttagttt gtatttagtt - 1561 gttaagtttt ttataatcat atgttaatga ggaattagct atatgatatc actgattgat - 1621 tggctatttt taggttaagt aattgtagtt aaatagttgt gttaagttag tatgttaagg - 1681 tttataggtt aagatttact aacaatcata ttatgtcatt agatgtaaat ttcattcctg - 1741 gcttgcttct gctttcgcat tgctaaccta caacaagact acctcaccca ctacccctcc - 1801 cctattctac ctcaacacat actacctcac atttgatttt tcttgattgc ttttcaagga - 1861 gcatactact a -// diff --git a/andv/nextclade/S/sequences.fasta b/andv/nextclade/S/sequences.fasta deleted file mode 100644 index 5cdfd94..0000000 --- a/andv/nextclade/S/sequences.fasta +++ /dev/null @@ -1,33 +0,0 @@ ->NC_003466.1 Andes virus segment S, complete sequence -TAGTAGTAGACTCCTTGAGAAGCTACTGCTGCGAAAGCTGGAATGAGCACCCTCCAAGAA -TTGCAGGAAAACATCACAGCACACGAACAACAGCTCGTGACTGCTCGGCAAAAGCTTAAG -GATGCCGAGAAGGCAGTGGAGGTGGACCCGGATGACGTTAACAAGAGCACACTACAAAGT -AGACGGGCAGCTGTGTCTACATTGGAGACCAAACTCGGAGAACTTAAGAGGCAACTTGCA -GATTTGGTGGCAGCTCAAAAATTGGCTACAAAACCAGTTGATCCAACAGGGCTTGAGCCT -GATGATCATCTAAAGGAAAAATCATCTCTGAGATATGGGAATGTCCTGGATGTTAATTCA -ATTGATTTGGAAGAACCGAGTGGACAGACTGCTGATTGGAAGGCTATAGGAGCATACATC -TTAGGGTTTGCAATTCCGATCATCCTAAAGGCCTTATACATGCTGTCAACCCGTGGGAGA -CAAACTGTGAAAGACAACAAAGGGACCAGGATAAGGTTTAAGGATGATTCTTCCTTTGAA -GAAGTCAATGGGATACGTAAACCAAAACACCTTTACGTCTCAATGCCAACTGCACAGTCC -ACTATGAAGGCTGAAGAAATCACGCCAGGACGATTTAGGACAATTGCTTGTGGCCTTTTT -CCAGCACAGGTCAAAGCCCGAAATATAATAAGTCCTGTAATGGGAGTAATTGGATTTGGC -TTCTTTGTAAAGGATTGGATGGATCGGATAGAAGAGTTTCTGGCTGCAGAGTGTCCATTC -TTACCTAAGCCAAAGGTCGCCTCAGAAGCCTTCATGTCTACCAATAAGATGTATTTTCTG -AACAGACAGAGACAAGTCAATGAATCTAAGGTTCAAGATATTATCGATTTGATAGACCAT -GCTGAGACCGAGTCTGCTACCTTGTTTACAGAGATTGCAACACCCCATTCAGTCTGGGTG -TTTGCATGTGCACCTGACCGGTGCCCTCCAACTGCATTGTATGTTGCAGGGGTACCGGAA -CTTGGTGCATTTTTTTCTATCCTTCAGGACATGCGTAATACCATCATGGCATCTAAATCT -GTAGGGACTGCAGAAGAGAAGCTAAAGAAAAAATCTGCCTTCTACCAATCATACCTAAGA -AGGACACAATCTATGGGAATCCAACTGGACCAGAAGATCATAATCCTTTACATGCTATCA -TGGGGTAAAGAAGCTGTGAATCACTTCCATCTTGGTGATGATATGGACCCTGAACTCAGG -CAGCTAGCACAATCTCTGATCGATACTAAGGTGAAGGAGATCTCCAACCAAGAGCCACTT -AAGTTGTAGGTGCTTAATGAAATCATGATTGAAGAAAGACTTTCCGGGCTTGTGCCACAT -ATTAATCATCTCAGGACCTATCCTTAATGTGATTAATAGGGTTTTATTATAAGGGCAGTT -AATGGGGTTGGTTACTAACTATGGGTAAGGGTTCATTACCATTTTTGCACTAGGGTTAAA -GGGCCACTACATTGTATTTGCACTAAGGGAAATGGGAGGTGGGTTAGTTTGTATTTAGTT -GTTAAGTTTTTTATAATCATATGTTAATGAGGAATTAGCTATATGATATCACTGATTGAT -TGGCTATTTTTAGGTTAAGTAATTGTAGTTAAATAGTTGTGTTAAGTTAGTATGTTAAGG -TTTATAGGTTAAGATTTACTAACAATCATATTATGTCATTAGATGTAAATTTCATTCCTG -GCTTGCTTCTGCTTTCGCATTGCTAACCTACAACAAGACTACCTCACCCACTACCCCTCC -CCTATTCTACCTCAACACATACTACCTCACATTTGATTTTTCTTGATTGCTTTTCAAGGA -GCATACTACTA diff --git a/andv/nextclade_data/andv/L/unreleased/CHANGELOG.md b/andv/nextclade_data/andv/L/unreleased/CHANGELOG.md deleted file mode 100644 index 0f72c1e..0000000 --- a/andv/nextclade_data/andv/L/unreleased/CHANGELOG.md +++ /dev/null @@ -1,5 +0,0 @@ -# Changelog - -## 2026-05-08 - -Initial minimal dataset generated from NCBI GenBank reference annotation. diff --git a/andv/nextclade_data/andv/L/unreleased/README.md b/andv/nextclade_data/andv/L/unreleased/README.md deleted file mode 100644 index fcfadb1..0000000 --- a/andv/nextclade_data/andv/L/unreleased/README.md +++ /dev/null @@ -1,3 +0,0 @@ -# Andes virus L segment - -Minimal Nextclade dataset for Andes virus L segment using Andes virus reference. diff --git a/andv/nextclade_data/andv/L/unreleased/dataset.zip b/andv/nextclade_data/andv/L/unreleased/dataset.zip deleted file mode 100644 index f05cb3f..0000000 Binary files a/andv/nextclade_data/andv/L/unreleased/dataset.zip and /dev/null differ diff --git a/andv/nextclade_data/andv/L/unreleased/genome_annotation.gff3 b/andv/nextclade_data/andv/L/unreleased/genome_annotation.gff3 deleted file mode 100644 index 2671f79..0000000 --- a/andv/nextclade_data/andv/L/unreleased/genome_annotation.gff3 +++ /dev/null @@ -1,7 +0,0 @@ -##gff-version 3 -#!gff-spec-version 1.21 -#!processor NCBI annotwriter -##sequence-region NC_003468.2 1 6562 -##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1980456 -NC_003468.2 RefSeq region 1 6562 . + . ID=NC_003468.2:1..6562;Dbxref=taxon:1980456;Name=L;gbkey=Src;genome=genomic;mol_type=genomic RNA;old-name=Andes virus;segment=L;strain=Chile-9717869 -NC_003468.2 RefSeq CDS 36 6497 . + 0 Name=RdRp;gbkey=CDS;locus_tag=ANDVsLgp1;protein_id=NP_604473.1;product=RNA polymerase;ID=cds-NP_604473.1;Dbxref=GenBank:NP_604473.1,GeneID:991234 diff --git a/andv/nextclade_data/andv/L/unreleased/pathogen.json b/andv/nextclade_data/andv/L/unreleased/pathogen.json deleted file mode 100644 index 96758f5..0000000 --- a/andv/nextclade_data/andv/L/unreleased/pathogen.json +++ /dev/null @@ -1,39 +0,0 @@ -{ - "$schema": "https://raw.githubusercontent.com/nextstrain/nextclade/refs/heads/release/packages/nextclade-schemas/input-pathogen-json.schema.json", - "schemaVersion": "3.0.0", - "files": { - "reference": "reference.fasta", - "pathogenJson": "pathogen.json", - "genomeAnnotation": "genome_annotation.gff3", - "examples": "sequences.fasta", - "readme": "README.md", - "changelog": "CHANGELOG.md" - }, - "attributes": { - "name": "Andes virus L", - "reference name": "Andes virus segment L", - "reference accession": "NC_003468.2" - }, - "qc": { - "missingData": { - "enabled": true, - "missingDataThreshold": 2000, - "scoreBias": 500 - }, - "snpClusters": { - "enabled": false - }, - "mixedSites": { - "enabled": true, - "mixedSitesThreshold": 15 - }, - "frameShifts": { - "enabled": true, - "scoreWeight": 20 - }, - "stopCodons": { - "enabled": true, - "scoreWeight": 50 - } - } -} diff --git a/andv/nextclade_data/andv/L/unreleased/reference.fasta b/andv/nextclade_data/andv/L/unreleased/reference.fasta deleted file mode 100644 index 30c0f8f..0000000 --- a/andv/nextclade_data/andv/L/unreleased/reference.fasta +++ /dev/null @@ -1,111 +0,0 @@ ->NC_003468.2 Andes virus segment L, complete genome -TAGTAGTAGACTCCGGGATAGAAAAAGTTAGAAAAATGGAAAAGTATAGAGAGATTCATC -AGAGAGTTAGGGACCTTGCACCTGGAACGGTATCAGCATTAGAATGCATAGATCTACTGG -ATAGGCTCTACGCTGTCAGACATGACCTGGTTGACCAGATGATAAAACATGACTGGTCTG -ATAATAAAGATGTAGAAAGACCTATAGGTCAAGTTTTACTGATGGCTGGCATACCTAATG -ATATTATACAAGGCATGGAGAAGAAGATTATACCAAATAGCCCTTCTGGACAAGTATTGA -AAAGCTTTTTCCGAATGACACCAGATAATTATAAAATTACAGGTAACTTGATTGAGTTTA -TTGAAGTGACTGTAACAGCTGATGTGTCACGAGGTATTAGGGAGAAGAAAATAAAGTATG -AAGGAGGCCTCCAATTTGTTGAGCACTTACTGGAAACTGAATCAAGGAAGGGTAATATAC -CGCAACCTTATAAAATAACATTCTCAGTGGTTGCAGTTAAAACAGATGGATCAAACATCT -CGACTCAGTGGCCCAGTCGGAGGAACGATGGGGTAGTTCAGCACATGCGTCTAGTCCAAG -CTGATATAAATTATGTCAGAGAGCATTTAATAAAGTTAGATGAGAGAGCATCTTTGGAGG -CAATGTTTAACTTAAAGTTCCATGTATCAGGCCCTAAACTGAGATACTTTAACATCCCTG -ATTATAGACCACAGCAGCTATGTGAACCACGGATTGACAACTTAATACAATATTGCAAGA -ATTGGTTGACAAAAGAACATAAGTTTGTATTCAAAGAAGTCAGTGGAGCTAATGTGATTC -AAGCATTTGAGAGTCATGAACAGTTACATTTACAGAAATACAACGAATCACGAAAACCAA -GAAATTTTTTACTCTTGCAGCTTACAGTGCAAGGGGCATATCTACCATCAACAATCAGTT -CTGACCAGTGCAATACTAGGATTGGGTGTCTAGAAATATCAAAAAACCAACCAGAAACAC -CAGTACAGATGCTTGCATTGGATATATCTTATAAGTATCTGAGTCTTACAAGGGATGAGT -TGATCAATTATTATAGCCCTAGAGTGCACTTTCAATCGAGCCCTAATGTGAAGGAACCAG -GGACACTGAAGTTAGGATTATCACAATTAAATCCACTCTCTAAATCAATTCTTGACAATG -TTGGAAAGCATAAAAAGGATAAAGGATTATTTGGTGAGATCATAGATAGCATAAATGTGG -CAAGTCAAATACAGATCAATGCATGTGCAAAAATAATTGAGCAGATCTTATCAAATCTTG -AAATAAACATTGGAGAAATAAATGCTAGTATGCCTTCTCCTAATAAGACAACAGGTGTAG -ATGACCTGTTAAATAAATTTTATGATAATGAGCTTGGTAAATATATGTTATCCATTCTGA -GGAAAACAGCAGCATGGCATATAGGCCATCTAGTCAGAGATATCACAGAAAGTTTAATTG -CACATGCTGGGCTGCGCCGTTCTAAATATTGGTCAGTACATGCATATGACCATGGGAATG -TAATTTTGTTTATCTTGCCATCAAAGTCACTAGAGGTAGTAGGTTCTTATATAAGGTATT -TCACAGTATTTAAAGATGGTATAGGGTTGATAGACGCAGATAATATTGATTCTAAGGCCG -AAATTGATGGTGTCACCTGGTGTTATTCTAAGGTCATGAGTATTGATTTAAACAGGTTAT -TGGCTTTGAACATAGCTTTTGAGAAGTCACTTCTTGCCACGGCTACATGGTTCCAATATT -ATACTGAAGACCAAGGCCATTTTCCCCTTCAACATGCATTAAGGTCAATCTTTTCTTTCC -ACTTTTTACTCTGTGTGTCACAAAAGATGAAGCTATGTGCAATATTTGATAACCTTCGTT -ATCTGATACCATCAGTAACATCTTTGTACTCTGGGTACGAGTTGTTAATAGAAAAATTCT -TTGAGAGACCATTTAAGAGTTCACTGGATGTATACCTTTATTCTATCATAAAATCTCTAT -TAATTAGTTTGGCACAAAATAATAAAGTTCGATTTTACTCAAGAGTTCGTTTGTTAGGAT -TGACAGTTGATCACTCCACGGTCGGAGCAAGTGGTGTTTACCCCTCTTTAATGTCCCGTG -TTGTTTACAAACATTACAGAAGTTTAATCTCTGAAGCTACAACTTGTTTTTTCTTATTTG -AAAAGGGTTTGCATGGGAATTTACCAGAAGAGGCTAAAATACATCTTGAAACCATTGAAT -GGGCTCGGAAGTTCCAGGAGAAAGAAAAACAATATGGTGATATTCTTCTAAAGGAAGGCT -ATACAATTGAATCTGTAATCAATGGAGAAGTTGATGTAGAACAACAGCTTTTTTGTCAGG -AGGTCTCAGAGCTAAGTGCACAAGAGCTCAACAAATATTTACAGGCAAAATCTCAAGTTT -TATGTGCTAATATCATGAATAAACACTGGGACAAACCATATTTCAGTCAAACACGCAATA -TCAGTCTCAAGGGAATGTCTGGGGCATTGCAAGAGGATGGACATTTAGCTGCTAGTGTGA -CACTGATTGAAGCAATTAGGTTTTTAAATAGATCACAAACCAATCCAAATGTTATTGATA -TGTATGAGCAGACTAAACAATCAAAGGCACAAGCTAGGATTGTTAGGAAATACCAGAGAA -CAGAAGCAGATAGAGGATTTTTTATCACAACATTACCAACTAGGGTGCGATTAGAAATAA -TAGAAGATTATTTCGATGCAATTGCAAAGGTTGTGCCTGAAGAATATATTTCTTATGGTG -GGGATAAAAAAGTTCTAAATATTCAGAATGCACTAGAGAAAGCACTTAGATGGGCATCTG -GAGTATCAGAAATTACAACAAGCACTGGTAAAAGCATCAAGTTTAAGCGGAAATTAATGT -ATGTTAGTGCTGATGCCACAAAATGGTCACCAGGAGATAATTCTGCTAAGTTTAGGAGAT -TTACACAAGCAATATATGATGGCTTATCAGACAACAAACTGAAATGTTGTGTTGTTGATG -CATTACGTAACATTTATGAGACTGAATTTTTTATGTCCAGGAAATTACACCGATATATTG -ATAGTATGGAAAATCATTCAGATGCGGTTGAAGATTTCTTGGCATTTTTCTCAAATGGAG -TCTCAGCCAATGTAAAGGGAAACTGGCTTCAAGGGAACTTAAATAAATGCTCATCATTAT -TTGGTGCTGCTGTCTCATTACTTTTTCGGGAGGTCTGGAAACAATTGTTTCCAGAATTAG -AGTGTTTTTTTGAATTTGCACATCATTCAGATGATGCATTGTTCATTTATGGCTATCTGG -AGCCTGAAGATGATGGAACAGATTGGTTTTTGTATGTATCACAGCAGATACAGGCAGGAA -ACTTTCATTGGCATGCTATAAATCAAGAGATGTGGAAGAGCATGTTTAATCTACATGAGC -ACTTACTATTAATGGGTTCTATTAAAGTGTCACCTAAGAAGACAACAGTATCACCTACTA -ATGCAGAATTTCTTTCTACTTTTTTTGAAGGTTGTGCTGTGTCAATCCCTTTTGTTAAAA -TCTTACTGGGTTCATTATCAGATCTTCCTGGGTTAGGTTTCTTTGATGATTTAGCAGCAG -CACAAAGCAGATGTGTAAAGTCACTAGATTTGGGTGCTTGCCCACAATTAGCTCAACTAG -CTATAGTATTATGCACAAGCAAAGTTGAGAGGTTGTATGGTACTGCTGATGGAATGGTAA -ACTCTCCAACAGCATTCCTTAAGGTGAATAAAGCACACGTACCAGTACCACTTGGTGGTG -ATGGCTCAATGTCTATTATGGAGCTTGCAACAGCTGGTTTTGGGATGGCAGATAAGAATA -TTTTAAAAAATGCATTCATATCTTATAAGCATACTCGTAGAGATGGTGATAGGTACGTAT -TGGGTTTATTTAAATTTTTGATGTCATTAAGTGAGGATGTATTCCAGCACGACCGATTGG -GTGAGTTTAGTTTTGTAGGTAAAGTTCAATGGAAAGTGTTCACTCCTAAAGCTGAATTTG -AATTTCATGATCAATTTTCACATAATTATTTATTAGAGTGGACACGTCAACATCCTGTGT -ATGACTATATTATTCCTAGAAATAGAGATAATTTGCTTGTATACCTTGTAAGAAAGTTGA -ATGATCCTAGCATCATTACAGCTATGACTATGCAGTCACCATTACAACTTCGTTTCCGTA -TGCAAGCAAAGCAACATATGAAAGTATGCCGGTATGAAGGTGAATGGGTCACATTCAGGG -AGGTACTTGCTGCAGCTGATAGTTTTGCTACGAGTTACCAACCTACTGAAAGGGACATGG -ATCTCTTTAATACACTTGTAAGTTGTACATTTTCTAAAGAGTATGCTTGGAAAGACTTTT -TAAATGAAGTAAGGTGTGAGGTCTTAACAACAAGACATGTACATAGGCCTAAAATTGCTA -GGACATTCACTGTTAGAGAAAAGGACCAGGCTATACAAAATCCAATAAATTCGGTGATTG -GCTATAAGTATGCTCTTACAGTGGATGAAGTCAGTGATGTTCTTGATAGTGCATTCTTCC -CAGAGTCTCTATCTGCAGACTTACAGGTTATGAAAGATGGAGTTTACAGAGAATTAGGAC -TTGATATAAGTTCTCCTGAAGTCCTAAAACGCATAGCACCACTATTATATAAGGCAGGAA -GGTCACGTGTTGTTATTGTGGAAGGAAATGTAGAAGGGACAGCTGAGTCAATCTGTAGTT -ATTGGCTCAAGACAATGTCACTGATTAAAACAATCAGAGTAAGACCTAAGAAGGAGGTAC -TGAAAGCTATGTCTTTATATAGTGTTAAAGAAAATATTGGATTGCAGGATGATATTGCAG -CAACTCGACTATGCATAGAAATCTGGAGATGGTGTAAGGCAAATGAACAGGATGTTAAAG -AATGGCTAACATCTCTGTACTTTGAAAAACAGACATTGATGGATTGGGTAGAAAGGTTTA -GAAGGAAAGGAGTTGTTCCTATTGATCCTGAAATACAATGTATTGGCCTACTCTTATATG -ATGTATTAGGTTATAAAAGTGTGTTACAAATGCAAGCAAACCGAAGAGCCTATTCAGGTA -AGCAATATGATGCATACTGTGTGCAAACATATAACGAGGAAACAAAACTATATGAAGGTG -ACCTTCGTGTTACTTTTAATTTTGGTTTAGATTGTGCAAGGTTAGAAGTTTTTTGGGATA -AAAAAGAGTATATCTTAGAGACATCTATCACCCAACGACATGTGTTGCGGTTACTGATGG -AAGAAGTGTCACAAGAATTAATTAGATGTGGAATGAGATTCAAAACAGAGCAAGTCAATC -AAACTCGGAGCTTAGTGTTATTCAAAACAGAGGCTGGTTTTGAATGGGGTAAGCCTAATG -TGCCATGTATTGTATATAAACACTGTGTCTTGAGAACTGGGCTTCGTACGAAACAGCCAA -TTAATAAAGAGTTCATGATAAATGTACAAAGTGATGGTTTCCGTGCAATAGCACAGATGG -ATATTGAGAGTCCACGGTTCTTGTTAGCACATGCATATCATACACTGCGTGATATTAGAT -ATCAAGCAGTGCAGGCAGTAGGGAATGTATGGTTTAAAACAGAACAGCACAAACTATTTA -TTAACCCAATTATATCATCAGGGCTTTTAGAAAACTTTATGAAAGGCTTACCTGCTGCCA -TACCTCCTGCTGCATATTCCCTCATAATGAACAAGGCTAAGATTTCTGTGGATTTGTTTA -TGTTCAATGAGCTATTAGCACTTATAAATAGGAATAATATCCTCAACCTTGATGGGATTG -AAGAAACATCTGAAGGTTATAGTACTGTGACATCAATGTCTAGCAAGCAGTGGTCTGAAG -AGATGAGTTTAATGTCTGATGATGATATTGATGATATGGAGGACTTTACTATAGCACTGG -ATGATATTGACTTTGAACAAATAAATTTGGAAGAGGATATACAACACTTTCTGCAGGATG -AATCAGCATATGTTGGTGATTTATTGATTCAGACAGAAGACATTGAGGTTAAAAAGATAC -GTGGGGTGACAAGAGTATTAGAGCCAGTCAAGCTATTAAAAAGCTGGGTTTCTAAAGGCC -TTGCTATAGACAAAGTATACAATCCTATCGGGATAATCTTAATGGCAAGATACATGTCAA -AAACATACAATTTCAGTTCAACACCTCTTGCACTATTAAATCCATATGACTTGACAGAAC -TTGAAAGTGTTGTAAAGGGATGGGGAGAAACTGTAAATGATCGATTCAAAGATTTAGATA -TTGAGGCACAAACAGTTGTTAAAGAAAAGGGTGTACAGCCAGAAGATGTACTCCCTGATT -CATTATTCTCTTTCAGGCATGTTGATGTTTTGCTGCGAAGGTTGTTCCCGCGTGACCCTG -TATCAACATTCTATTAGTGGATTTTATACCTTATTCATACAGTATGTATATTGTAGTGTT -CTTTTCCCGGAGCATACTACTA diff --git a/andv/nextclade_data/andv/L/unreleased/sequences.fasta b/andv/nextclade_data/andv/L/unreleased/sequences.fasta deleted file mode 100644 index 30c0f8f..0000000 --- a/andv/nextclade_data/andv/L/unreleased/sequences.fasta +++ /dev/null @@ -1,111 +0,0 @@ ->NC_003468.2 Andes virus segment L, complete genome -TAGTAGTAGACTCCGGGATAGAAAAAGTTAGAAAAATGGAAAAGTATAGAGAGATTCATC -AGAGAGTTAGGGACCTTGCACCTGGAACGGTATCAGCATTAGAATGCATAGATCTACTGG -ATAGGCTCTACGCTGTCAGACATGACCTGGTTGACCAGATGATAAAACATGACTGGTCTG -ATAATAAAGATGTAGAAAGACCTATAGGTCAAGTTTTACTGATGGCTGGCATACCTAATG -ATATTATACAAGGCATGGAGAAGAAGATTATACCAAATAGCCCTTCTGGACAAGTATTGA -AAAGCTTTTTCCGAATGACACCAGATAATTATAAAATTACAGGTAACTTGATTGAGTTTA -TTGAAGTGACTGTAACAGCTGATGTGTCACGAGGTATTAGGGAGAAGAAAATAAAGTATG -AAGGAGGCCTCCAATTTGTTGAGCACTTACTGGAAACTGAATCAAGGAAGGGTAATATAC -CGCAACCTTATAAAATAACATTCTCAGTGGTTGCAGTTAAAACAGATGGATCAAACATCT -CGACTCAGTGGCCCAGTCGGAGGAACGATGGGGTAGTTCAGCACATGCGTCTAGTCCAAG -CTGATATAAATTATGTCAGAGAGCATTTAATAAAGTTAGATGAGAGAGCATCTTTGGAGG -CAATGTTTAACTTAAAGTTCCATGTATCAGGCCCTAAACTGAGATACTTTAACATCCCTG -ATTATAGACCACAGCAGCTATGTGAACCACGGATTGACAACTTAATACAATATTGCAAGA -ATTGGTTGACAAAAGAACATAAGTTTGTATTCAAAGAAGTCAGTGGAGCTAATGTGATTC -AAGCATTTGAGAGTCATGAACAGTTACATTTACAGAAATACAACGAATCACGAAAACCAA -GAAATTTTTTACTCTTGCAGCTTACAGTGCAAGGGGCATATCTACCATCAACAATCAGTT -CTGACCAGTGCAATACTAGGATTGGGTGTCTAGAAATATCAAAAAACCAACCAGAAACAC -CAGTACAGATGCTTGCATTGGATATATCTTATAAGTATCTGAGTCTTACAAGGGATGAGT -TGATCAATTATTATAGCCCTAGAGTGCACTTTCAATCGAGCCCTAATGTGAAGGAACCAG -GGACACTGAAGTTAGGATTATCACAATTAAATCCACTCTCTAAATCAATTCTTGACAATG -TTGGAAAGCATAAAAAGGATAAAGGATTATTTGGTGAGATCATAGATAGCATAAATGTGG -CAAGTCAAATACAGATCAATGCATGTGCAAAAATAATTGAGCAGATCTTATCAAATCTTG -AAATAAACATTGGAGAAATAAATGCTAGTATGCCTTCTCCTAATAAGACAACAGGTGTAG -ATGACCTGTTAAATAAATTTTATGATAATGAGCTTGGTAAATATATGTTATCCATTCTGA -GGAAAACAGCAGCATGGCATATAGGCCATCTAGTCAGAGATATCACAGAAAGTTTAATTG -CACATGCTGGGCTGCGCCGTTCTAAATATTGGTCAGTACATGCATATGACCATGGGAATG -TAATTTTGTTTATCTTGCCATCAAAGTCACTAGAGGTAGTAGGTTCTTATATAAGGTATT -TCACAGTATTTAAAGATGGTATAGGGTTGATAGACGCAGATAATATTGATTCTAAGGCCG -AAATTGATGGTGTCACCTGGTGTTATTCTAAGGTCATGAGTATTGATTTAAACAGGTTAT -TGGCTTTGAACATAGCTTTTGAGAAGTCACTTCTTGCCACGGCTACATGGTTCCAATATT -ATACTGAAGACCAAGGCCATTTTCCCCTTCAACATGCATTAAGGTCAATCTTTTCTTTCC -ACTTTTTACTCTGTGTGTCACAAAAGATGAAGCTATGTGCAATATTTGATAACCTTCGTT -ATCTGATACCATCAGTAACATCTTTGTACTCTGGGTACGAGTTGTTAATAGAAAAATTCT -TTGAGAGACCATTTAAGAGTTCACTGGATGTATACCTTTATTCTATCATAAAATCTCTAT -TAATTAGTTTGGCACAAAATAATAAAGTTCGATTTTACTCAAGAGTTCGTTTGTTAGGAT -TGACAGTTGATCACTCCACGGTCGGAGCAAGTGGTGTTTACCCCTCTTTAATGTCCCGTG -TTGTTTACAAACATTACAGAAGTTTAATCTCTGAAGCTACAACTTGTTTTTTCTTATTTG -AAAAGGGTTTGCATGGGAATTTACCAGAAGAGGCTAAAATACATCTTGAAACCATTGAAT -GGGCTCGGAAGTTCCAGGAGAAAGAAAAACAATATGGTGATATTCTTCTAAAGGAAGGCT -ATACAATTGAATCTGTAATCAATGGAGAAGTTGATGTAGAACAACAGCTTTTTTGTCAGG -AGGTCTCAGAGCTAAGTGCACAAGAGCTCAACAAATATTTACAGGCAAAATCTCAAGTTT -TATGTGCTAATATCATGAATAAACACTGGGACAAACCATATTTCAGTCAAACACGCAATA -TCAGTCTCAAGGGAATGTCTGGGGCATTGCAAGAGGATGGACATTTAGCTGCTAGTGTGA -CACTGATTGAAGCAATTAGGTTTTTAAATAGATCACAAACCAATCCAAATGTTATTGATA -TGTATGAGCAGACTAAACAATCAAAGGCACAAGCTAGGATTGTTAGGAAATACCAGAGAA -CAGAAGCAGATAGAGGATTTTTTATCACAACATTACCAACTAGGGTGCGATTAGAAATAA -TAGAAGATTATTTCGATGCAATTGCAAAGGTTGTGCCTGAAGAATATATTTCTTATGGTG -GGGATAAAAAAGTTCTAAATATTCAGAATGCACTAGAGAAAGCACTTAGATGGGCATCTG -GAGTATCAGAAATTACAACAAGCACTGGTAAAAGCATCAAGTTTAAGCGGAAATTAATGT -ATGTTAGTGCTGATGCCACAAAATGGTCACCAGGAGATAATTCTGCTAAGTTTAGGAGAT -TTACACAAGCAATATATGATGGCTTATCAGACAACAAACTGAAATGTTGTGTTGTTGATG -CATTACGTAACATTTATGAGACTGAATTTTTTATGTCCAGGAAATTACACCGATATATTG -ATAGTATGGAAAATCATTCAGATGCGGTTGAAGATTTCTTGGCATTTTTCTCAAATGGAG -TCTCAGCCAATGTAAAGGGAAACTGGCTTCAAGGGAACTTAAATAAATGCTCATCATTAT -TTGGTGCTGCTGTCTCATTACTTTTTCGGGAGGTCTGGAAACAATTGTTTCCAGAATTAG -AGTGTTTTTTTGAATTTGCACATCATTCAGATGATGCATTGTTCATTTATGGCTATCTGG -AGCCTGAAGATGATGGAACAGATTGGTTTTTGTATGTATCACAGCAGATACAGGCAGGAA -ACTTTCATTGGCATGCTATAAATCAAGAGATGTGGAAGAGCATGTTTAATCTACATGAGC -ACTTACTATTAATGGGTTCTATTAAAGTGTCACCTAAGAAGACAACAGTATCACCTACTA -ATGCAGAATTTCTTTCTACTTTTTTTGAAGGTTGTGCTGTGTCAATCCCTTTTGTTAAAA -TCTTACTGGGTTCATTATCAGATCTTCCTGGGTTAGGTTTCTTTGATGATTTAGCAGCAG -CACAAAGCAGATGTGTAAAGTCACTAGATTTGGGTGCTTGCCCACAATTAGCTCAACTAG -CTATAGTATTATGCACAAGCAAAGTTGAGAGGTTGTATGGTACTGCTGATGGAATGGTAA -ACTCTCCAACAGCATTCCTTAAGGTGAATAAAGCACACGTACCAGTACCACTTGGTGGTG -ATGGCTCAATGTCTATTATGGAGCTTGCAACAGCTGGTTTTGGGATGGCAGATAAGAATA -TTTTAAAAAATGCATTCATATCTTATAAGCATACTCGTAGAGATGGTGATAGGTACGTAT -TGGGTTTATTTAAATTTTTGATGTCATTAAGTGAGGATGTATTCCAGCACGACCGATTGG -GTGAGTTTAGTTTTGTAGGTAAAGTTCAATGGAAAGTGTTCACTCCTAAAGCTGAATTTG -AATTTCATGATCAATTTTCACATAATTATTTATTAGAGTGGACACGTCAACATCCTGTGT -ATGACTATATTATTCCTAGAAATAGAGATAATTTGCTTGTATACCTTGTAAGAAAGTTGA -ATGATCCTAGCATCATTACAGCTATGACTATGCAGTCACCATTACAACTTCGTTTCCGTA -TGCAAGCAAAGCAACATATGAAAGTATGCCGGTATGAAGGTGAATGGGTCACATTCAGGG -AGGTACTTGCTGCAGCTGATAGTTTTGCTACGAGTTACCAACCTACTGAAAGGGACATGG -ATCTCTTTAATACACTTGTAAGTTGTACATTTTCTAAAGAGTATGCTTGGAAAGACTTTT -TAAATGAAGTAAGGTGTGAGGTCTTAACAACAAGACATGTACATAGGCCTAAAATTGCTA -GGACATTCACTGTTAGAGAAAAGGACCAGGCTATACAAAATCCAATAAATTCGGTGATTG -GCTATAAGTATGCTCTTACAGTGGATGAAGTCAGTGATGTTCTTGATAGTGCATTCTTCC -CAGAGTCTCTATCTGCAGACTTACAGGTTATGAAAGATGGAGTTTACAGAGAATTAGGAC -TTGATATAAGTTCTCCTGAAGTCCTAAAACGCATAGCACCACTATTATATAAGGCAGGAA -GGTCACGTGTTGTTATTGTGGAAGGAAATGTAGAAGGGACAGCTGAGTCAATCTGTAGTT -ATTGGCTCAAGACAATGTCACTGATTAAAACAATCAGAGTAAGACCTAAGAAGGAGGTAC -TGAAAGCTATGTCTTTATATAGTGTTAAAGAAAATATTGGATTGCAGGATGATATTGCAG -CAACTCGACTATGCATAGAAATCTGGAGATGGTGTAAGGCAAATGAACAGGATGTTAAAG -AATGGCTAACATCTCTGTACTTTGAAAAACAGACATTGATGGATTGGGTAGAAAGGTTTA -GAAGGAAAGGAGTTGTTCCTATTGATCCTGAAATACAATGTATTGGCCTACTCTTATATG -ATGTATTAGGTTATAAAAGTGTGTTACAAATGCAAGCAAACCGAAGAGCCTATTCAGGTA -AGCAATATGATGCATACTGTGTGCAAACATATAACGAGGAAACAAAACTATATGAAGGTG -ACCTTCGTGTTACTTTTAATTTTGGTTTAGATTGTGCAAGGTTAGAAGTTTTTTGGGATA -AAAAAGAGTATATCTTAGAGACATCTATCACCCAACGACATGTGTTGCGGTTACTGATGG -AAGAAGTGTCACAAGAATTAATTAGATGTGGAATGAGATTCAAAACAGAGCAAGTCAATC -AAACTCGGAGCTTAGTGTTATTCAAAACAGAGGCTGGTTTTGAATGGGGTAAGCCTAATG -TGCCATGTATTGTATATAAACACTGTGTCTTGAGAACTGGGCTTCGTACGAAACAGCCAA -TTAATAAAGAGTTCATGATAAATGTACAAAGTGATGGTTTCCGTGCAATAGCACAGATGG -ATATTGAGAGTCCACGGTTCTTGTTAGCACATGCATATCATACACTGCGTGATATTAGAT -ATCAAGCAGTGCAGGCAGTAGGGAATGTATGGTTTAAAACAGAACAGCACAAACTATTTA -TTAACCCAATTATATCATCAGGGCTTTTAGAAAACTTTATGAAAGGCTTACCTGCTGCCA -TACCTCCTGCTGCATATTCCCTCATAATGAACAAGGCTAAGATTTCTGTGGATTTGTTTA -TGTTCAATGAGCTATTAGCACTTATAAATAGGAATAATATCCTCAACCTTGATGGGATTG -AAGAAACATCTGAAGGTTATAGTACTGTGACATCAATGTCTAGCAAGCAGTGGTCTGAAG -AGATGAGTTTAATGTCTGATGATGATATTGATGATATGGAGGACTTTACTATAGCACTGG -ATGATATTGACTTTGAACAAATAAATTTGGAAGAGGATATACAACACTTTCTGCAGGATG -AATCAGCATATGTTGGTGATTTATTGATTCAGACAGAAGACATTGAGGTTAAAAAGATAC -GTGGGGTGACAAGAGTATTAGAGCCAGTCAAGCTATTAAAAAGCTGGGTTTCTAAAGGCC -TTGCTATAGACAAAGTATACAATCCTATCGGGATAATCTTAATGGCAAGATACATGTCAA -AAACATACAATTTCAGTTCAACACCTCTTGCACTATTAAATCCATATGACTTGACAGAAC -TTGAAAGTGTTGTAAAGGGATGGGGAGAAACTGTAAATGATCGATTCAAAGATTTAGATA -TTGAGGCACAAACAGTTGTTAAAGAAAAGGGTGTACAGCCAGAAGATGTACTCCCTGATT -CATTATTCTCTTTCAGGCATGTTGATGTTTTGCTGCGAAGGTTGTTCCCGCGTGACCCTG -TATCAACATTCTATTAGTGGATTTTATACCTTATTCATACAGTATGTATATTGTAGTGTT -CTTTTCCCGGAGCATACTACTA diff --git a/andv/nextclade_data/andv/M/unreleased/CHANGELOG.md b/andv/nextclade_data/andv/M/unreleased/CHANGELOG.md deleted file mode 100644 index 0f72c1e..0000000 --- a/andv/nextclade_data/andv/M/unreleased/CHANGELOG.md +++ /dev/null @@ -1,5 +0,0 @@ -# Changelog - -## 2026-05-08 - -Initial minimal dataset generated from NCBI GenBank reference annotation. diff --git a/andv/nextclade_data/andv/M/unreleased/README.md b/andv/nextclade_data/andv/M/unreleased/README.md deleted file mode 100644 index 36d518e..0000000 --- a/andv/nextclade_data/andv/M/unreleased/README.md +++ /dev/null @@ -1,3 +0,0 @@ -# Andes virus M segment - -Minimal Nextclade dataset for Andes virus M segment using Andes virus reference. diff --git a/andv/nextclade_data/andv/M/unreleased/dataset.zip b/andv/nextclade_data/andv/M/unreleased/dataset.zip deleted file mode 100644 index 22e378c..0000000 Binary files a/andv/nextclade_data/andv/M/unreleased/dataset.zip and /dev/null differ diff --git a/andv/nextclade_data/andv/M/unreleased/genome_annotation.gff3 b/andv/nextclade_data/andv/M/unreleased/genome_annotation.gff3 deleted file mode 100644 index 63806f7..0000000 --- a/andv/nextclade_data/andv/M/unreleased/genome_annotation.gff3 +++ /dev/null @@ -1,7 +0,0 @@ -##gff-version 3 -#!gff-spec-version 1.21 -#!processor NCBI annotwriter -##sequence-region NC_003467.2 1 3671 -##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1980456 -NC_003467.2 RefSeq region 1 3671 . + . ID=NC_003467.2:1..3671;Dbxref=taxon:1980456;Name=M;gbkey=Src;genome=genomic;mol_type=genomic RNA;old-name=Andes virus;segment=M;strain=Chile-9717869 -NC_003467.2 RefSeq CDS 52 3468 . + 0 Name=GPC;gbkey=CDS;locus_tag=ANDVsMgp1;protein_id=NP_604472.1;ID=cds-NP_604472.1;Dbxref=GenBank:NP_604472.1,GeneID:991233;product=G1 and G2 surface glycoprotein precursor diff --git a/andv/nextclade_data/andv/M/unreleased/pathogen.json b/andv/nextclade_data/andv/M/unreleased/pathogen.json deleted file mode 100644 index 5d5c6d1..0000000 --- a/andv/nextclade_data/andv/M/unreleased/pathogen.json +++ /dev/null @@ -1,39 +0,0 @@ -{ - "$schema": "https://raw.githubusercontent.com/nextstrain/nextclade/refs/heads/release/packages/nextclade-schemas/input-pathogen-json.schema.json", - "schemaVersion": "3.0.0", - "files": { - "reference": "reference.fasta", - "pathogenJson": "pathogen.json", - "genomeAnnotation": "genome_annotation.gff3", - "examples": "sequences.fasta", - "readme": "README.md", - "changelog": "CHANGELOG.md" - }, - "attributes": { - "name": "Andes virus M", - "reference name": "Andes virus segment M", - "reference accession": "NC_003467.2" - }, - "qc": { - "missingData": { - "enabled": true, - "missingDataThreshold": 2000, - "scoreBias": 500 - }, - "snpClusters": { - "enabled": false - }, - "mixedSites": { - "enabled": true, - "mixedSitesThreshold": 15 - }, - "frameShifts": { - "enabled": true, - "scoreWeight": 20 - }, - "stopCodons": { - "enabled": true, - "scoreWeight": 50 - } - } -} diff --git a/andv/nextclade_data/andv/M/unreleased/reference.fasta b/andv/nextclade_data/andv/M/unreleased/reference.fasta deleted file mode 100644 index 57fb40b..0000000 --- a/andv/nextclade_data/andv/M/unreleased/reference.fasta +++ /dev/null @@ -1,63 +0,0 @@ ->NC_003467.2 Andes virus segment M, complete genome -TAGTAGTAGACTCCGCAAGAAGAAGCAAAAAATTAAAGAAGTGAGTTTAAAATGGAAGGG -TGGTATCTGGTTGTTCTTGGAGTCTGCTATACGCTGACACTGGCAATGCCCAAGACCATT -TATGAGCTTAAAATGGAATGCCCGCACACTGTGGGTCTCGGTCAAGGTTACATCATTGGC -TCAACAGAACTAGGTTTGATCTCAATTGAGGCTGCATCTGATATAAAGCTCGAGAGCTCT -TGCAATTTTGATCTTCATACAACATCTATGGCCCAGAAGAGTTTCACCCAAGTTGAATGG -AGAAAGAAAAGTGACACAACTGATACCACAAATGCTGCGTCCACTACCTTTGAAGCACAA -ACTAAAACTGTTAACCTTAGAGGGACTTGTATACTGGCACCTGAACTCTATGATACATTG -AAGAAAGTAAAAAAGACAGTCCTGTGCTATGATCTAACATGTAATCAAACACATTGTCAG -CCAACTGTCTATCTGATTGCACCTGTATTGACATGCATGTCAATAAGAAGTTGTATGGCT -AGTGTGTTTACAAGCAGGATTCAGGTGATTTATGAAAAGACACATTGTGTAACAGGTCAG -CTGATTGAGGGTCAGTGTTTCAACCCAGCACACACATTGACATTATCTCAGCCTGCTCAC -ACTTATGATACTGTCACCCTTCCTATCTCTTGTTTTTTCACACCAAAGAAGTCGGAGCAA -CTAAAAGTTATAAAAACATTTGAAGGAATTCTGACGAAGACAGGTTGCACGGAGAATGCA -TTGCAGGGTTATTATGTGTGTTTTTTAGGGAGTCATTCAGAACCTTTAATTGTTCCGAGT -TTGGAGGACATACGGTCTGCTGAAGTTGTTAGTAGGATGCTTGTACACCCTAGGGGAGAA -GACCATGATGCCATACAGAATTCACAAAGTCACTTAAGAATAGTGGGACCTATCACAGCA -AAAGTGCCATCAACTAGTTCCACAGATACCCTAAAGGGGACAGCCTTTGCAGGCGTCCCA -ATGTATAGCTCTTTATCTACACTAGTCAGAAATGCAGACCCAGAATTTGTATTTTCTCCA -GGTATAGTACCTGAATCTAATCACAGTACATGTGATAAGAAGACAGTACCTATCACATGG -ACAGGCTACCTACCAATATCAGGTGAGATGGAAAAAGTGACTGGATGTACAGTTTTTTGT -ACACTAGCAGGACCTGGTGCTAGTTGTGAGGCCTATTCTGAAAATGGTATATTTAACATC -AGTTCTCCAACATGTCTTGTAAACAAAGTCCAAAGATTTCGTGGATCTGAACAGAAAATA -AATTTTATCTGTCAGCGGGTAGATCAGGATGTTGTTGTATACTGCAATGGGCAAAAGAAA -GTCATATTAACCAAAACTTTGGTTATTGGGCAGTGTATTTATACATTCACAAGCCTATTT -TCATTGATGCCTGATGTAGCCCACTCATTGGCTGTAGAATTATGTGTCCCGGGATTACAT -GGATGGGCCACTGTCATGCTTCTATCAACATTCTGCTTTGGGTGGGTCTTGATTCCTGCG -GTCACATTAATAATATTAAAGTGTCTAAGGGTTTTGACGTTTTCTTGTTCCCATTACACT -AATGAGTCAAAATTTAAATTCATCCTGGAAAAAGTTAAAATTGAATACCAAAAGACTATG -GGATCAATGGTGTGCGATGTATGTCATCATGAGTGTGAAACAGCAAAAGAACTTGAATCA -CATAGACAGAGTTGTATCAATGGACAATGTCCTTATTGCATGACAATAACTGAAGCAACT -GAAAGTGCCTTGCAAGCCCATTATTCCATTTGTAAATTGACAGGAAGATTTCAGGAGGCA -CTGAAAAAGTCACTTAAAAAGCCAGAGGTAAAAAAAGGTTGTTACAGAACACTCGGGGTA -TTTAGATATAAAAGTAGATGTTATGTGGGTTTGGTATGGTGCCTATTGTTGACATGTGAA -ATTGTTATTTGGGCCGCAAGTGCAGAGACTCCACTAATGGAGTCAGGCTGGTCAGATACG -GCTCATGGTGTTGGTGAGATTCCAATGAAGACAGACCTCGAGCTGGACTTTTCACTGCCT -TCTTCATCCTCTTACAGTTATAGGAGAAAGCTCACAAACCCAGCCAATAAAGAAGAGTCT -ATTCCCTTCCACTTCCAGATGGAAAAACAAGTAATTCATGCTGAAATCCAACCCCTGGGT -CATTGGATGGATGCGACATTTAATATTAAGACTGCATTTCATTGTTATGGTGCATGCCAG -AAATACTCTTATCCATGGCAGACATCTAAGTGCTTCTTTGAAAAGGACTACCAGTATGAA -ACAGGCTGGGGCTGTAATCCTGGTGACTGCCCAGGGGTTGGGACTGGATGCACTGCTTGT -GGTGTTTATCTCGATAAACTAAAATCTGTTGGGAAGGCCTATAAGATAATTTCTTTAAAA -TATACCAGAAAGGTTTGTATTCAGTTAGGAACAGAACAAACTTGCAAGCATATTGATGCA -AATGATTGTTTAGTGACACCATCTGTGAAAGTTTGCATAGTGGGCACAGTTTCAAAACTT -CAACCATCTGATACTCTTTTGTTCTTAGGTCCACTAGAACAAGGGGGAATCATTCTTAAG -CAATGGTGCACAACATCATGTGCATTTGGGGACCCTGGTGATATCATGTCCACTCCCAGT -GGTATGAGGTGTCCAGAGCACACTGGATCATTTAGGAAAATTTGCGGTTTTGCTACTACA -CCAGTTTGTGAATATCAAGGAAATACCATTTCTGGATATAAAAGAATGATGGCAACAAAA -GATTCATTCCAATCATTTAACTTAACAGAACCTCACATCACAACAAACAAGCTTGAATGG -ATCGACCCAGATGGGAATACAAGAGACCACGTAAACCTTGTCTTAAATAGAGATGTCTCA -TTTCAGGATTTAAGTGATAACCCCTGTAAAGTAGACCTACACACACAAGCAATAGAAGGG -GCATGGGGTTCTGGTGTAGGGTTTACACTCACATGTACTGTCGGATTAACAGAGTGCCCA -AGTTTTATGACATCAATTAAGGCATGTGACCTAGCTATGTGTTATGGATCAACAGTAACA -AACCTTGCCAGGGGCTCTAATACAGTGAAAGTAGTTGGTAAAGGAGGCCATTCAGGGTCC -TCATTTAAATGCTGTCATGATACAGATTGCTCCTCTGAAGGTTTACTTGCATCAGCCCCT -CATCTTGAGAGGGTAACAGGATTCAATCAAATTGATTCAGATAAGGTTTATGATGATGGT -GCACCACCTTGCACATTCAAATGCTGGTTCACTAAGTCAGGTGAGTGGCTTCTTGGGATC -TTAAACGGGAATTGGATTGTTGTTGTAGTGCTTGTTGTGATACTCATTCTCTCTATCATA -ATGTTCAGTGTTTTGTGTCCCAGGAGAGGGCACAAGAAAACTGTCTAAGCATTGACCTCA -ACTCCTACATTAGATCATATACATTTATGCACTTCCTCATATTTAGCTGCACTAAGATAT -TAATAAACTCTAGTTATTGACTTTATAAGATTATTATGGAACTAACCTCACTTAAAAAAA -ACAAATACTTTACTCATATATAACTCCATATTCTCTTACCGAGGCTTTTGTTCCTGCGGA -GCATACTACTA diff --git a/andv/nextclade_data/andv/M/unreleased/sequences.fasta b/andv/nextclade_data/andv/M/unreleased/sequences.fasta deleted file mode 100644 index 57fb40b..0000000 --- a/andv/nextclade_data/andv/M/unreleased/sequences.fasta +++ /dev/null @@ -1,63 +0,0 @@ ->NC_003467.2 Andes virus segment M, complete genome -TAGTAGTAGACTCCGCAAGAAGAAGCAAAAAATTAAAGAAGTGAGTTTAAAATGGAAGGG -TGGTATCTGGTTGTTCTTGGAGTCTGCTATACGCTGACACTGGCAATGCCCAAGACCATT -TATGAGCTTAAAATGGAATGCCCGCACACTGTGGGTCTCGGTCAAGGTTACATCATTGGC -TCAACAGAACTAGGTTTGATCTCAATTGAGGCTGCATCTGATATAAAGCTCGAGAGCTCT -TGCAATTTTGATCTTCATACAACATCTATGGCCCAGAAGAGTTTCACCCAAGTTGAATGG -AGAAAGAAAAGTGACACAACTGATACCACAAATGCTGCGTCCACTACCTTTGAAGCACAA -ACTAAAACTGTTAACCTTAGAGGGACTTGTATACTGGCACCTGAACTCTATGATACATTG -AAGAAAGTAAAAAAGACAGTCCTGTGCTATGATCTAACATGTAATCAAACACATTGTCAG -CCAACTGTCTATCTGATTGCACCTGTATTGACATGCATGTCAATAAGAAGTTGTATGGCT -AGTGTGTTTACAAGCAGGATTCAGGTGATTTATGAAAAGACACATTGTGTAACAGGTCAG -CTGATTGAGGGTCAGTGTTTCAACCCAGCACACACATTGACATTATCTCAGCCTGCTCAC -ACTTATGATACTGTCACCCTTCCTATCTCTTGTTTTTTCACACCAAAGAAGTCGGAGCAA -CTAAAAGTTATAAAAACATTTGAAGGAATTCTGACGAAGACAGGTTGCACGGAGAATGCA -TTGCAGGGTTATTATGTGTGTTTTTTAGGGAGTCATTCAGAACCTTTAATTGTTCCGAGT -TTGGAGGACATACGGTCTGCTGAAGTTGTTAGTAGGATGCTTGTACACCCTAGGGGAGAA -GACCATGATGCCATACAGAATTCACAAAGTCACTTAAGAATAGTGGGACCTATCACAGCA -AAAGTGCCATCAACTAGTTCCACAGATACCCTAAAGGGGACAGCCTTTGCAGGCGTCCCA -ATGTATAGCTCTTTATCTACACTAGTCAGAAATGCAGACCCAGAATTTGTATTTTCTCCA -GGTATAGTACCTGAATCTAATCACAGTACATGTGATAAGAAGACAGTACCTATCACATGG -ACAGGCTACCTACCAATATCAGGTGAGATGGAAAAAGTGACTGGATGTACAGTTTTTTGT -ACACTAGCAGGACCTGGTGCTAGTTGTGAGGCCTATTCTGAAAATGGTATATTTAACATC -AGTTCTCCAACATGTCTTGTAAACAAAGTCCAAAGATTTCGTGGATCTGAACAGAAAATA -AATTTTATCTGTCAGCGGGTAGATCAGGATGTTGTTGTATACTGCAATGGGCAAAAGAAA -GTCATATTAACCAAAACTTTGGTTATTGGGCAGTGTATTTATACATTCACAAGCCTATTT -TCATTGATGCCTGATGTAGCCCACTCATTGGCTGTAGAATTATGTGTCCCGGGATTACAT -GGATGGGCCACTGTCATGCTTCTATCAACATTCTGCTTTGGGTGGGTCTTGATTCCTGCG -GTCACATTAATAATATTAAAGTGTCTAAGGGTTTTGACGTTTTCTTGTTCCCATTACACT -AATGAGTCAAAATTTAAATTCATCCTGGAAAAAGTTAAAATTGAATACCAAAAGACTATG -GGATCAATGGTGTGCGATGTATGTCATCATGAGTGTGAAACAGCAAAAGAACTTGAATCA -CATAGACAGAGTTGTATCAATGGACAATGTCCTTATTGCATGACAATAACTGAAGCAACT -GAAAGTGCCTTGCAAGCCCATTATTCCATTTGTAAATTGACAGGAAGATTTCAGGAGGCA -CTGAAAAAGTCACTTAAAAAGCCAGAGGTAAAAAAAGGTTGTTACAGAACACTCGGGGTA -TTTAGATATAAAAGTAGATGTTATGTGGGTTTGGTATGGTGCCTATTGTTGACATGTGAA -ATTGTTATTTGGGCCGCAAGTGCAGAGACTCCACTAATGGAGTCAGGCTGGTCAGATACG -GCTCATGGTGTTGGTGAGATTCCAATGAAGACAGACCTCGAGCTGGACTTTTCACTGCCT -TCTTCATCCTCTTACAGTTATAGGAGAAAGCTCACAAACCCAGCCAATAAAGAAGAGTCT -ATTCCCTTCCACTTCCAGATGGAAAAACAAGTAATTCATGCTGAAATCCAACCCCTGGGT -CATTGGATGGATGCGACATTTAATATTAAGACTGCATTTCATTGTTATGGTGCATGCCAG -AAATACTCTTATCCATGGCAGACATCTAAGTGCTTCTTTGAAAAGGACTACCAGTATGAA -ACAGGCTGGGGCTGTAATCCTGGTGACTGCCCAGGGGTTGGGACTGGATGCACTGCTTGT -GGTGTTTATCTCGATAAACTAAAATCTGTTGGGAAGGCCTATAAGATAATTTCTTTAAAA -TATACCAGAAAGGTTTGTATTCAGTTAGGAACAGAACAAACTTGCAAGCATATTGATGCA -AATGATTGTTTAGTGACACCATCTGTGAAAGTTTGCATAGTGGGCACAGTTTCAAAACTT -CAACCATCTGATACTCTTTTGTTCTTAGGTCCACTAGAACAAGGGGGAATCATTCTTAAG -CAATGGTGCACAACATCATGTGCATTTGGGGACCCTGGTGATATCATGTCCACTCCCAGT -GGTATGAGGTGTCCAGAGCACACTGGATCATTTAGGAAAATTTGCGGTTTTGCTACTACA -CCAGTTTGTGAATATCAAGGAAATACCATTTCTGGATATAAAAGAATGATGGCAACAAAA -GATTCATTCCAATCATTTAACTTAACAGAACCTCACATCACAACAAACAAGCTTGAATGG -ATCGACCCAGATGGGAATACAAGAGACCACGTAAACCTTGTCTTAAATAGAGATGTCTCA -TTTCAGGATTTAAGTGATAACCCCTGTAAAGTAGACCTACACACACAAGCAATAGAAGGG -GCATGGGGTTCTGGTGTAGGGTTTACACTCACATGTACTGTCGGATTAACAGAGTGCCCA -AGTTTTATGACATCAATTAAGGCATGTGACCTAGCTATGTGTTATGGATCAACAGTAACA -AACCTTGCCAGGGGCTCTAATACAGTGAAAGTAGTTGGTAAAGGAGGCCATTCAGGGTCC -TCATTTAAATGCTGTCATGATACAGATTGCTCCTCTGAAGGTTTACTTGCATCAGCCCCT -CATCTTGAGAGGGTAACAGGATTCAATCAAATTGATTCAGATAAGGTTTATGATGATGGT -GCACCACCTTGCACATTCAAATGCTGGTTCACTAAGTCAGGTGAGTGGCTTCTTGGGATC -TTAAACGGGAATTGGATTGTTGTTGTAGTGCTTGTTGTGATACTCATTCTCTCTATCATA -ATGTTCAGTGTTTTGTGTCCCAGGAGAGGGCACAAGAAAACTGTCTAAGCATTGACCTCA -ACTCCTACATTAGATCATATACATTTATGCACTTCCTCATATTTAGCTGCACTAAGATAT -TAATAAACTCTAGTTATTGACTTTATAAGATTATTATGGAACTAACCTCACTTAAAAAAA -ACAAATACTTTACTCATATATAACTCCATATTCTCTTACCGAGGCTTTTGTTCCTGCGGA -GCATACTACTA diff --git a/andv/nextclade_data/andv/S/unreleased/CHANGELOG.md b/andv/nextclade_data/andv/S/unreleased/CHANGELOG.md deleted file mode 100644 index 0f72c1e..0000000 --- a/andv/nextclade_data/andv/S/unreleased/CHANGELOG.md +++ /dev/null @@ -1,5 +0,0 @@ -# Changelog - -## 2026-05-08 - -Initial minimal dataset generated from NCBI GenBank reference annotation. diff --git a/andv/nextclade_data/andv/S/unreleased/README.md b/andv/nextclade_data/andv/S/unreleased/README.md deleted file mode 100644 index 69ed153..0000000 --- a/andv/nextclade_data/andv/S/unreleased/README.md +++ /dev/null @@ -1,3 +0,0 @@ -# Andes virus S segment - -Minimal Nextclade dataset for Andes virus S segment using Andes virus reference. diff --git a/andv/nextclade_data/andv/S/unreleased/dataset.zip b/andv/nextclade_data/andv/S/unreleased/dataset.zip deleted file mode 100644 index f2e15a0..0000000 Binary files a/andv/nextclade_data/andv/S/unreleased/dataset.zip and /dev/null differ diff --git a/andv/nextclade_data/andv/S/unreleased/genome_annotation.gff3 b/andv/nextclade_data/andv/S/unreleased/genome_annotation.gff3 deleted file mode 100644 index 2f0415f..0000000 --- a/andv/nextclade_data/andv/S/unreleased/genome_annotation.gff3 +++ /dev/null @@ -1,8 +0,0 @@ -##gff-version 3 -#!gff-spec-version 1.21 -#!processor NCBI annotwriter -##sequence-region NC_003466.1 1 1871 -##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1980456 -NC_003466.1 RefSeq region 1 1871 . + . ID=NC_003466.1:1..1871;Dbxref=taxon:1980456;Name=S;gbkey=Src;genome=genomic;mol_type=viral cRNA;old-name=Andes virus;segment=S;strain=Chile-9717869 -NC_003466.1 RefSeq CDS 43 1329 . + 0 Name=N;gbkey=CDS;locus_tag=ANDVsSgp1;protein_id=NP_604471.1;ID=cds-NP_604471.1;product=nucleocapsid protein;Dbxref=GenBank:NP_604471.1,GeneID:991232 -NC_003466.1 RefSeq CDS 122 313 . + 0 Name=NSs;gbkey=CDS;locus_tag=ANDVsSgp2;protein_id=YP_004928151.1;ID=cds-YP_004928151.1;product=putative nonstructural protein;Dbxref=GenBank:YP_004928151.1,GeneID:11293630 diff --git a/andv/nextclade_data/andv/S/unreleased/pathogen.json b/andv/nextclade_data/andv/S/unreleased/pathogen.json deleted file mode 100644 index 37414f8..0000000 --- a/andv/nextclade_data/andv/S/unreleased/pathogen.json +++ /dev/null @@ -1,39 +0,0 @@ -{ - "$schema": "https://raw.githubusercontent.com/nextstrain/nextclade/refs/heads/release/packages/nextclade-schemas/input-pathogen-json.schema.json", - "schemaVersion": "3.0.0", - "files": { - "reference": "reference.fasta", - "pathogenJson": "pathogen.json", - "genomeAnnotation": "genome_annotation.gff3", - "examples": "sequences.fasta", - "readme": "README.md", - "changelog": "CHANGELOG.md" - }, - "attributes": { - "name": "Andes virus S", - "reference name": "Andes virus segment S", - "reference accession": "NC_003466.1" - }, - "qc": { - "missingData": { - "enabled": true, - "missingDataThreshold": 2000, - "scoreBias": 500 - }, - "snpClusters": { - "enabled": false - }, - "mixedSites": { - "enabled": true, - "mixedSitesThreshold": 15 - }, - "frameShifts": { - "enabled": true, - "scoreWeight": 20 - }, - "stopCodons": { - "enabled": true, - "scoreWeight": 50 - } - } -} diff --git a/andv/nextclade_data/andv/S/unreleased/reference.fasta b/andv/nextclade_data/andv/S/unreleased/reference.fasta deleted file mode 100644 index 5cdfd94..0000000 --- a/andv/nextclade_data/andv/S/unreleased/reference.fasta +++ /dev/null @@ -1,33 +0,0 @@ ->NC_003466.1 Andes virus segment S, complete sequence -TAGTAGTAGACTCCTTGAGAAGCTACTGCTGCGAAAGCTGGAATGAGCACCCTCCAAGAA -TTGCAGGAAAACATCACAGCACACGAACAACAGCTCGTGACTGCTCGGCAAAAGCTTAAG -GATGCCGAGAAGGCAGTGGAGGTGGACCCGGATGACGTTAACAAGAGCACACTACAAAGT -AGACGGGCAGCTGTGTCTACATTGGAGACCAAACTCGGAGAACTTAAGAGGCAACTTGCA -GATTTGGTGGCAGCTCAAAAATTGGCTACAAAACCAGTTGATCCAACAGGGCTTGAGCCT -GATGATCATCTAAAGGAAAAATCATCTCTGAGATATGGGAATGTCCTGGATGTTAATTCA -ATTGATTTGGAAGAACCGAGTGGACAGACTGCTGATTGGAAGGCTATAGGAGCATACATC -TTAGGGTTTGCAATTCCGATCATCCTAAAGGCCTTATACATGCTGTCAACCCGTGGGAGA -CAAACTGTGAAAGACAACAAAGGGACCAGGATAAGGTTTAAGGATGATTCTTCCTTTGAA -GAAGTCAATGGGATACGTAAACCAAAACACCTTTACGTCTCAATGCCAACTGCACAGTCC -ACTATGAAGGCTGAAGAAATCACGCCAGGACGATTTAGGACAATTGCTTGTGGCCTTTTT -CCAGCACAGGTCAAAGCCCGAAATATAATAAGTCCTGTAATGGGAGTAATTGGATTTGGC -TTCTTTGTAAAGGATTGGATGGATCGGATAGAAGAGTTTCTGGCTGCAGAGTGTCCATTC -TTACCTAAGCCAAAGGTCGCCTCAGAAGCCTTCATGTCTACCAATAAGATGTATTTTCTG -AACAGACAGAGACAAGTCAATGAATCTAAGGTTCAAGATATTATCGATTTGATAGACCAT -GCTGAGACCGAGTCTGCTACCTTGTTTACAGAGATTGCAACACCCCATTCAGTCTGGGTG -TTTGCATGTGCACCTGACCGGTGCCCTCCAACTGCATTGTATGTTGCAGGGGTACCGGAA -CTTGGTGCATTTTTTTCTATCCTTCAGGACATGCGTAATACCATCATGGCATCTAAATCT -GTAGGGACTGCAGAAGAGAAGCTAAAGAAAAAATCTGCCTTCTACCAATCATACCTAAGA -AGGACACAATCTATGGGAATCCAACTGGACCAGAAGATCATAATCCTTTACATGCTATCA -TGGGGTAAAGAAGCTGTGAATCACTTCCATCTTGGTGATGATATGGACCCTGAACTCAGG -CAGCTAGCACAATCTCTGATCGATACTAAGGTGAAGGAGATCTCCAACCAAGAGCCACTT -AAGTTGTAGGTGCTTAATGAAATCATGATTGAAGAAAGACTTTCCGGGCTTGTGCCACAT -ATTAATCATCTCAGGACCTATCCTTAATGTGATTAATAGGGTTTTATTATAAGGGCAGTT -AATGGGGTTGGTTACTAACTATGGGTAAGGGTTCATTACCATTTTTGCACTAGGGTTAAA -GGGCCACTACATTGTATTTGCACTAAGGGAAATGGGAGGTGGGTTAGTTTGTATTTAGTT -GTTAAGTTTTTTATAATCATATGTTAATGAGGAATTAGCTATATGATATCACTGATTGAT -TGGCTATTTTTAGGTTAAGTAATTGTAGTTAAATAGTTGTGTTAAGTTAGTATGTTAAGG -TTTATAGGTTAAGATTTACTAACAATCATATTATGTCATTAGATGTAAATTTCATTCCTG -GCTTGCTTCTGCTTTCGCATTGCTAACCTACAACAAGACTACCTCACCCACTACCCCTCC -CCTATTCTACCTCAACACATACTACCTCACATTTGATTTTTCTTGATTGCTTTTCAAGGA -GCATACTACTA diff --git a/andv/nextclade_data/andv/S/unreleased/sequences.fasta b/andv/nextclade_data/andv/S/unreleased/sequences.fasta deleted file mode 100644 index 5cdfd94..0000000 --- a/andv/nextclade_data/andv/S/unreleased/sequences.fasta +++ /dev/null @@ -1,33 +0,0 @@ ->NC_003466.1 Andes virus segment S, complete sequence -TAGTAGTAGACTCCTTGAGAAGCTACTGCTGCGAAAGCTGGAATGAGCACCCTCCAAGAA -TTGCAGGAAAACATCACAGCACACGAACAACAGCTCGTGACTGCTCGGCAAAAGCTTAAG -GATGCCGAGAAGGCAGTGGAGGTGGACCCGGATGACGTTAACAAGAGCACACTACAAAGT -AGACGGGCAGCTGTGTCTACATTGGAGACCAAACTCGGAGAACTTAAGAGGCAACTTGCA -GATTTGGTGGCAGCTCAAAAATTGGCTACAAAACCAGTTGATCCAACAGGGCTTGAGCCT -GATGATCATCTAAAGGAAAAATCATCTCTGAGATATGGGAATGTCCTGGATGTTAATTCA -ATTGATTTGGAAGAACCGAGTGGACAGACTGCTGATTGGAAGGCTATAGGAGCATACATC -TTAGGGTTTGCAATTCCGATCATCCTAAAGGCCTTATACATGCTGTCAACCCGTGGGAGA -CAAACTGTGAAAGACAACAAAGGGACCAGGATAAGGTTTAAGGATGATTCTTCCTTTGAA -GAAGTCAATGGGATACGTAAACCAAAACACCTTTACGTCTCAATGCCAACTGCACAGTCC -ACTATGAAGGCTGAAGAAATCACGCCAGGACGATTTAGGACAATTGCTTGTGGCCTTTTT -CCAGCACAGGTCAAAGCCCGAAATATAATAAGTCCTGTAATGGGAGTAATTGGATTTGGC -TTCTTTGTAAAGGATTGGATGGATCGGATAGAAGAGTTTCTGGCTGCAGAGTGTCCATTC -TTACCTAAGCCAAAGGTCGCCTCAGAAGCCTTCATGTCTACCAATAAGATGTATTTTCTG -AACAGACAGAGACAAGTCAATGAATCTAAGGTTCAAGATATTATCGATTTGATAGACCAT -GCTGAGACCGAGTCTGCTACCTTGTTTACAGAGATTGCAACACCCCATTCAGTCTGGGTG -TTTGCATGTGCACCTGACCGGTGCCCTCCAACTGCATTGTATGTTGCAGGGGTACCGGAA -CTTGGTGCATTTTTTTCTATCCTTCAGGACATGCGTAATACCATCATGGCATCTAAATCT -GTAGGGACTGCAGAAGAGAAGCTAAAGAAAAAATCTGCCTTCTACCAATCATACCTAAGA -AGGACACAATCTATGGGAATCCAACTGGACCAGAAGATCATAATCCTTTACATGCTATCA -TGGGGTAAAGAAGCTGTGAATCACTTCCATCTTGGTGATGATATGGACCCTGAACTCAGG -CAGCTAGCACAATCTCTGATCGATACTAAGGTGAAGGAGATCTCCAACCAAGAGCCACTT -AAGTTGTAGGTGCTTAATGAAATCATGATTGAAGAAAGACTTTCCGGGCTTGTGCCACAT -ATTAATCATCTCAGGACCTATCCTTAATGTGATTAATAGGGTTTTATTATAAGGGCAGTT -AATGGGGTTGGTTACTAACTATGGGTAAGGGTTCATTACCATTTTTGCACTAGGGTTAAA -GGGCCACTACATTGTATTTGCACTAAGGGAAATGGGAGGTGGGTTAGTTTGTATTTAGTT -GTTAAGTTTTTTATAATCATATGTTAATGAGGAATTAGCTATATGATATCACTGATTGAT -TGGCTATTTTTAGGTTAAGTAATTGTAGTTAAATAGTTGTGTTAAGTTAGTATGTTAAGG -TTTATAGGTTAAGATTTACTAACAATCATATTATGTCATTAGATGTAAATTTCATTCCTG -GCTTGCTTCTGCTTTCGCATTGCTAACCTACAACAAGACTACCTCACCCACTACCCCTCC -CCTATTCTACCTCAACACATACTACCTCACATTTGATTTTTCTTGATTGCTTTTCAAGGA -GCATACTACTA diff --git a/andv/nextclade_data/index.json b/andv/nextclade_data/index.json deleted file mode 100644 index 7610ebe..0000000 --- a/andv/nextclade_data/index.json +++ /dev/null @@ -1,158 +0,0 @@ -{ - "schemaVersion": "3.0.0", - "collections": [ - { - "meta": { - "id": "loculus-agent-store", - "title": "Loculus agent store datasets", - "description": "Minimal Nextclade datasets staged by automation for Loculus testing.", - "maintainers": [ - { - "name": "Loculus project", - "url": "https://github.com/loculus-project" - } - ], - "urls": [ - { - "name": "source", - "url": "https://github.com/pathoplexus/sequence_store" - } - ] - }, - "datasets": [ - { - "path": "andv/L", - "shortcuts": [ - "andv/L" - ], - "enabled": true, - "attributes": { - "name": "Andes virus L segment", - "reference name": "Andes virus segment L", - "reference accession": "NC_003468.2" - }, - "files": { - "changelog": "CHANGELOG.md", - "examples": "sequences.fasta", - "genomeAnnotation": "genome_annotation.gff3", - "pathogenJson": "pathogen.json", - "readme": "README.md", - "reference": "reference.fasta" - }, - "capabilities": { - "qc": [ - "frameShifts", - "missingData", - "mixedSites", - "stopCodons" - ] - }, - "versions": [ - { - "tag": "unreleased", - "compatibility": { - "cli": "3.0.0-alpha.0", - "web": "3.0.0-alpha.0" - } - } - ], - "version": { - "tag": "unreleased", - "compatibility": { - "cli": "3.0.0-alpha.0", - "web": "3.0.0-alpha.0" - } - } - }, - { - "path": "andv/M", - "shortcuts": [ - "andv/M" - ], - "enabled": true, - "attributes": { - "name": "Andes virus M segment", - "reference name": "Andes virus segment M", - "reference accession": "NC_003467.2" - }, - "files": { - "changelog": "CHANGELOG.md", - "examples": "sequences.fasta", - "genomeAnnotation": "genome_annotation.gff3", - "pathogenJson": "pathogen.json", - "readme": "README.md", - "reference": "reference.fasta" - }, - "capabilities": { - "qc": [ - "frameShifts", - "missingData", - "mixedSites", - "stopCodons" - ] - }, - "versions": [ - { - "tag": "unreleased", - "compatibility": { - "cli": "3.0.0-alpha.0", - "web": "3.0.0-alpha.0" - } - } - ], - "version": { - "tag": "unreleased", - "compatibility": { - "cli": "3.0.0-alpha.0", - "web": "3.0.0-alpha.0" - } - } - }, - { - "path": "andv/S", - "shortcuts": [ - "andv/S" - ], - "enabled": true, - "attributes": { - "name": "Andes virus S segment", - "reference name": "Andes virus segment S", - "reference accession": "NC_003466.1" - }, - "files": { - "changelog": "CHANGELOG.md", - "examples": "sequences.fasta", - "genomeAnnotation": "genome_annotation.gff3", - "pathogenJson": "pathogen.json", - "readme": "README.md", - "reference": "reference.fasta" - }, - "capabilities": { - "qc": [ - "frameShifts", - "missingData", - "mixedSites", - "stopCodons" - ] - }, - "versions": [ - { - "tag": "unreleased", - "compatibility": { - "cli": "3.0.0-alpha.0", - "web": "3.0.0-alpha.0" - } - } - ], - "version": { - "tag": "unreleased", - "compatibility": { - "cli": "3.0.0-alpha.0", - "web": "3.0.0-alpha.0" - } - } - } - ] - } - ] -}