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.


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**][1] as a standalone tool. Yet another approach is a combination of VirSorter2, CheckV and DRAM-v as detailed in [**this protocol**][2] 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.


  [1]: https://github.com/AnantharamanLab/VIBRANT
  [2]: https://www.protocols.io/view/viral-sequence-identification-sop-with-virsorter2-bwm5pc86