Exporting processed .qza reads into separate .fasta files for each sample

Hello! I am looking for help with processing my data from Fungal ITS1 amplicon sequencing.

I have demultiplexed, paired-end reads in .fastq format. I imported my data into QIIME2 (installed on a VirtualBox), cut the primers using cutadapt, joined the forward and reverse reads using vsearch join-pairs, and quality filtered them using quality-filter q-score. Now I would like to export my reads to run them through a classifier outside of QIIME2. My research group has previously used QIIME1 and exported our processed reads into separate .fasta formatted files for each sample. The separate files are important for our downstream processing through BLAST and FHiTINGS (as described: https://pubmed.ncbi.nlm.nih.gov/23765392/).

However, QIIME2 requires artifacts for read processing. Is there a way to export multiple .fasta formatted files (each containing the reads from only one sample) from a .qza?


I think first you can use export command to extract fastq.gz files by samples:

mkdir extracted-reads
qiime tools extract \
  --input-path reads.qza \
  --output-path extracted-reads/

After you can use any suitable tool by your choice outside of Qiime2 to convert fastq.gz files to fasta

Thank you this seems to work great!

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