Which sequence variants are in taxonomic groupings?

This may be easy to do, I just do not know of an appropriate means to achieve my basic objective; any help would be much appreciated.

I have completed some 16s paired end Illumina analysis on q2- in which I have essentially followed the Atacama/Moving Pictures pipeline using the dada2 QC, and taxonomy assignment via Naive Bayes classifier using the GG 13_8 99% OTU reference database. So, from the taxonomic groupings, I would like to determine which sequence variants from the rep seqs set are in each taxonomic group. For example, at taxa level 7, I have several sequence variants that have been diagnosed as g_Rickettsia s_; I would like to have a way to see which rep seq features are in this taxa assignment. Is there a way to do this?

Please let me know if additional information is needed.

Hi @nvtravan!

In QIIME 2 we can treat some artifacts as metadata. These are typically artifacts that you can think of as mapping some ID to some piece of data (like a spreadsheet). This includes almost everything we call FeatureData[...].

Additionally, we can merge metadata in QIIME 2 making it easy to pair up pieces of data by their ID. In fact we have a tutorial example that does exactly what you are trying to do, merge your rep-seqs with your taxonomy:


Let me know if that’s what you’re looking for!

Ah ha! Perfect, perfect, perfect, exactly what I was looking for! Thank you!

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