RdRp scan - identifying/detecting viruses- metagenomic workflow- need help

Question

[eric--carron]

Good afternoon fellow biologists,

I have just discovered the joy of bioinformatics on linux (and its frustrations). However, I don't really understand the workflow for the RdRp scan method to detect viruses. => https://doi.org/10.1093/ve/veac082 => FIGURE 10

For now: I have done a whole genome and small RNA sequencing from a pool of about 600 individuals (RNA extraction and purification). From those reads, I went through all the steps (quality control (trim) / alignment to host (.sam) / samtools (which I may need advice about the flags to select by the way) / SPADES.

Now I feel really stuck. Most of the tools to identify viruses or potential viruses don't work (sometimes can't even be installed) - -BLAST -GeNomad -HMMER

If anyone can help me out with proper examples/ scripts for the RdRp scan method, I would be extremely grateful. Happy to get tips too, on how you would do to detect existing/new viruses.

Best wishes.

[Ram]

Have you tried using conda? Install miniconda3 and you'll be able to install any (well, reasonable) software you need using conda install.

[eric--carron]

Hello Ram, Thank you for your reply. I have installed conda and mamba, which is even faster. Didn't work i am afraid. Probably because i am on windows linux subsystem I guess.

[Ram]

I think conda is also available for Windows, but I'm not familiar with WSL so my suggestions are not of much value anymore.