modified header names in PHAMB

[ShailNair]

Hi,

My assembled contigs have headers as

c_000003956504
c_000004841845
c_000004821562

which matches with the VAMB bin headers. But when I run PHAMB, I get bin headers as :

1470111
816445
3021234
1094390

How to get the PHAMB contig headers in the initial VAMB bin headers format?.

[joacjo]

Hi Shail

Can you send me a snapshot of your clusters.tsv file? And how many samples do you have?
I expect that there might a problem in the naming of your contigs.

The framework is designed to use the Sample-IDs from the header of contigs to keep track of where each viral-bin is from.

best,
Joachim

[ShailNair]

@joacjo I used a single co-assembled contigs file for binning. Here is the snapshot of the cluster.tsv file and phamb generated fna file

The cluster.tsv file has 1101140 records.

I followed the How to Run - not in parallel - quick and dirty tutorial.

Thank you.

[joacjo]

Hi Shail

Ah I see. The names of the entries in vamb_bins.fna matches the VAMB-cluster names. Remember the bins in the .fna file are concats of the VAMB cluster sequences.

Example: In your clusters.tsv you might have a cluster with multiple contigs:

cluster contig
99999 c_000000123
99999 c_000000321

If this cluster is predicted putative viral, the resulting name in the .fna file will be: 99999

Does this make sense?

Best,
Joachim

[ShailNair]

Thanks. that makes sense.
Thanks for this very helpful tool. We could extract a three times higher number of complete viral contigs (as per CheckV's rule) with PHAMB in comparison to VirSorter2, DeepVirFinder and viralVerify.