Can PHAMB be used directly for Virome analysis (enrichment of viral particles followed by sequencing) about phamb HOT 2 OPEN

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!

from phamb.

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

from phamb.