Popular viral Metagenomics data analysis tool in 2022?

Question

[boaty]

Hi guys,

I am looking for a solid tool for viral metagenomic data analysis, for virus profiling etc. I am new in this domaine, I read some papers which propose several tools, I need to pick one and stick on it. So It is better ask the community first. I found tool such as Virsorter, VirFinder,PPR-Meta,DeepVirFinder and VirionLang, have no idea which one is relatively the best.

Please help.

My Metagenomics data is from human fecal sample, medium depth. I've already run humann3 for shallow microbiome analysis. Yes, humann3(or metaphlan3) can do virus profiling with additional parameter --add_viruses, but results was not good enough.

Answer 1

[Mensur Dlakic]

I don't think there is a best tool for this purpose, as all of them them are better at one thing or another. Generally speaking, homology-based tools tend to have lower false positive rate, yet tools that rely on k-mer frequencies may work better in discovering novel and rare viruses. The most reliable solution is likely to come as a union of several approaches.

I recommend VIBRANT as a standalone tool. Yet another approach is a combination of VirSorter2, CheckV and DRAM-v as detailed in this protocol by Sullivan lab.

I don't think you need pleas for help in your messages. It is understood that everyone who writes in this forum needs help.

[boaty]

Thanks Mensur, I got it.

[boaty]

hi Meusur,

This is a feedback about your suggestion.

I tested your suggestions last week, here's what I found.

VIBRANT is great with its kegg database, everything is good to go. I decided to run my analysis with VIBRANT

For Virsorter2 pipeline : viral-id-sop, I found a lot of bugs. I spent days to manually modify its python code and snakemake code. But the DRAM-v really is time consuming step with too much needs for memory. Just can not spend a month for annotation.

Thanks again