Is it possible to extract 16S region from a whole bacterial genome using qiime2?

I want to extract the 16S rRNA region from a few whole bacterial genome sequences for taxonomy analysis. Is it possible to perform this action by using qiime2?


Hi @hongwei2017,
Do you specifically need to extract the 16S region or would you be ok with just working with the whole sequences and get taxonomy information? I ask because some q2 plugins like metaphlan2 or shogun might be of interest. For readily extracting the 16S region I can’t think of a qiime2 plugin from the top of my head that does this and has properly benchmarked the results but perhaps you can massage the the feature-classifier extract reads plugin to do this for you? You would need to input your representative sequences and input 16S region primers to extract the in between sequences. Not sure if that gets you where you need but might be a start?

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