Is there anyone working in virus bioinformatics here, and would be interested in having a particular virus specific tool made into an nf-core module?

I have a student, @Junhong Jia, who works with viruses in natural environments. I know he's been trying out #C0905QCFTPE a bit but it seems I haven't yet convinced him to take the full leap to automated pipelines. He might be missing some tools there.

If he has any, for the viral bioinformatics Hackathon what I'm looking for suggestoons I can give some of the participants to get module writing experience

I think he has mentioned missing tools. And I suggested he could get involved. Let's see if he replies.

Hi @James Fellows Yates, I have been working with viral isolates and just started touching upon viral metagenomes, most of my knowledge regarding metagenomics is theoretical but I can give some suggestions. Apart from assembling with metaviralSPAdes, viral contigs identification using geNomad, quality assessment using checkv, binning using vRhyme, functional annotation using first Pharokka then Phold. I am still not sure how to deal with taxonomic classification and mapping, maybe vContact3 could be good for taxonomic analysis. As for viral isolate, I use taxmyphage for phylogenetics, but it is only feasible with complete viral genome so not very possible with metagenome. I hope this helps.

OK! So of your list, not made as nf-core modules yet: • metaviralSPAdes • Phold • vContact3 • taxmypage Already • geNomad (endtoend) • checkv (endtoend) • vrhyme • Pharokka If you would be OK with it @Junhong Jia, I could potentially recruit various people to help make the not-yet-nf-core-modules so could be added to some pipelines ?

Sure.

I work mostly on targeted virus pathogens, but for virus metagenomics we often use the EsViritu pipeline for a quick check of which viruses we might have: cmmr/EsViritu: Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data In my experience, the virus metagenomics field is not as developed as for bacteria. And often the important choice is which database to use, not the specific tool. Also, the purpose of the analyses requires different strategies. If you want taxonomic identification and profiling or genome assemblies. And thanks for the description of your workflow Junhong Jia! Very useful to see these tools 🙂 I'm happy to contribute on these discussions.

Wait metaviralSPAdes is just an option within spades. So i don’t believe it needs to be a module.

Yes, I found that after