is it possible to use QIIME 2 to analyse viral genome ?


I write to you because wondering to know if it's possible to use QIIME 2 to analyse viral genome. If so, could you communicate to me the command ? If no, do you have any suggestion of commonly used pipeline for viral genome analysis and the database used for alignment ?


Hi @M_F,

Well, we do have some ongoing development of such tools, they are not necessarily full-featured at this time, but could help get you started.

In the RESCRIPt preprint, we provide an example of using sour-mash to compare HEV genomes. If you have RESCRIPt installed then all you need to do is install this specific PR for q2-sourmash. Here is the relevant notebook.

Also, there is the genome-sampler plugin, if you are interested in COVID genomes.

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Hi @SoilRotifer

Thank you

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