Taxonomy filtering Greengenes2


We are switching our workflows over to Greengenes2, and we are noticing something that seems weird to us. Normally, we filter out sequences from chloroplast and mitochondria after classifying our reads using the following command:

qiime taxa filter-table
--i-table table.qza
--i-taxonomy taxonomy.qza
--p-exclude 'chloroplast,mitochondria'
--o-filtered-table table-no-chloro-nomito.qza

However, after classifying reads using Greengenes2, this does not filter any sequences. I suppose it's possible that no sequences are being classified as mitochondria or chloroplast, but this seems odd for our samples (primate feces). Should we be using other terms to exclude mitochondrial and chloroplast sequences? Or is this something we no longer need to worry about with the switch to Greengenes2?


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Hi @emallott,

Thank you for checking in on this. We included mitochondria and chloroplast, but during the placement step rather and their labels were accidentally not included in the taxonomy decoration. I'm keenly aware of this issue, and am working on a revised taxonomy update. In the mean time, there are a few options, one would be to filter to the mitochondria / chloroplast records themselves specifically. The other option would be a prefilter against another database prior to use of GG2. I think the latter is a little easier, albeit obviously not ideal

Sorry for brevity, am limited on time this morning. Please let me know if expanded detail is needed.

All the best,


That makes sense, @wasade! Thanks for explaining what is going on and working on updating it!