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alexmsalmeida / virsearch

Snakemake workflow to detect and classify viruses in metagenome assemblies.
MIT License
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taxonomy #4

Open wuhuiyun07 opened 6 months ago

wuhuiyun07 commented 6 months ago

Hi!

I am doing similar virus discovery analysis with Snakemake as your work. I am wondering if you have published your work before? Do you have a plan to get family and genus level taxonomy information for your work?

Here is my repository: https://github.com/wuhuiyun07/pav_mgs_2023/tree/main/workflow/rules

Thanks!

alexmsalmeida commented 6 months ago

Hi,

We currently have a manuscript in press that has adapted and cited this pipeline for their study. However, I don't have any plans to have a dedicated paper for the tool itself.

It would be straightforward to add genus information in the pipeline (we already have taxonomy up to family). However, with the new ICTV nomenclature, most of the Orders and Families of metagenomic viruses are already unassigned at that level. I think there will need to be a larger community effort to generate new taxa for the wealth of viral data that is now out there (akin to what was done with GTDB for prokaryotes).

Thanks for sharing your repo.

Best, Alex