Can PHAMB be used directly for Virome analysis (enrichment of viral particles followed by sequencing)

[1023011930]

It's great to have virus binning software, you guys have made an excellent contribution. I would like to ask about the relationship of PHAMB with VirSorter2, VirFinder. Should I use VirFinder etc. to identify virus contigs first or should I use PHAMB to binning first?

[joacjo]

Hi - Thanks for the kind words!

First, the PHAMB approach was designed with Bulk metagenomics in mind, but the binning process and approach should work all the same on VLPs. However, if you are working with VLP samples, which usually contain a lot of random small bacterial chromosomal fragments/Junk, there might be a lot of value in performing a prefiltering step.

I would suggest:

• Identify virus like contigs for each sample using a more recent and fast tool such as GeNomad (https://github.com/apcamargo/genomad). This will also save a lot of time for the subsequent steps.
• Use these contigs as your starting point (i.e. contigs.fna.gz) for running VAMB and then PHAMB.

Hope this approach is helpful!

[1023011930]

Thanks for the advice, I'll try the workflow you recommend!