Is QIIME2 capable of analyzing shotgun sequences

I love QIIME2 for my amplicon sequencing analysis. But now I am moving towards doing more shotgun sequencing.

I saw on previous posts that q2 shogun or metaphan are some tools in QIIME2 that could be potentially useful. Have these improved?

I am mainly interested in looking at bacteria with a key interest in toxin and secondary metabolite production collected from the environment.

1 Like

Hi @Ellenphant,

I recategorized this to General Discussions as it wasn’t about a technical issue with Qiime2.

Could you clarify what you mean by

“Have these improved?”

Were you having issues with these plugins before or were waiting for any updates?

The q2-shogun plugin is meant for use with shallow-shotgun data otherwise I think q2-metaphlan is what you want to use. I can’t speak on their accuracy if that is what you are asking about, but recommend reading their respective papers/tutorial pages for more info.

1 Like