Exporting demultiplexed fna file

I am trying to figure out how to export a demultiplexed and concatentated fna file from Qiime2 in order to combine with other fna files in order to run a bayesian model outside of Qiime2. Any help would be greatly appreciated.

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Hi @Jarrad_Marcell,

Welcome to the forum!
Qiime2 artifacts are simply zip files that contain your data plus its associated metadata file. You can unzip them just like a regular zipped file and grab your data from the ‘data’ folder.
You can also do this via Qiime2 using the export/extract commands. See this tutorial for more details.


I understand that you can export/extract your qza files, but I don’t see the qiime2 code that actually generates a demultiplexed fasta to do this.

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Hey @Jarrad_Marcell, great question! If you have a SampleData[SequencesWithQuality | JoinedSequencesWithQuality] artifact, you’re in luck:

qiime tools export \
  --input-path demux.qza \
  --output-path seqs_fna_dir \
  --output-format QIIME1DemuxDirFmt

As @Mehrbod_Estaki implied above, if you already have a SampleData[Sequences] artifact, you can export as-is, leaving off the --output-format flag.

Hope that helps!

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Thanks guys. It’s much appreciated.

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