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.
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.