Quality filtering from fna input

i have some older IonTorrent data I need to work with and only have the .fna file (2 lines per read in fasta format). I can import that data into qiime2 without a problem and perform the dereplicating. When I look at my biom table I have a LOT of singletons and low frequency ASVs that I want to filter out. As a relative newbie, what is the best way to filter out these ASVs before downstream processing? I’m following the Moving Picture tutorial with success, just snagged here.


Good morning Russell,

Thanks for checking in on the forums!

For filtering, try this:

A small tip: Vsearch works best with shor accurate amplicons, like those made by Illumina. For Ion Torrent, try replacing vsearch OTUs with DADA2 ASVs. That should help a lot.

Let us know what you find,


Thanks! The filtering made life a lot easier. Turns out I was misunderstanding the features versus sequences notion of the syntax.

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Ah, got it. “Features” are the general name for OTUs/ASVs in the feature-abundance table.

If you are really into the words, there is a comprehensive review of how Qiime 2 works here, with plenty of emojis :point_down: :stuck_out_tongue_winking_eye:

Thanks for getting started with Qiime 2! If this question is answered, you can select the Solution :white_check_mark: or pass out some :heart:s


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If it’s words that @Russell_Minton is interested in, the glossary would be more helpful than the overview tutorial:

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