ASVs and their associated FASTA files

Hi Qiime2 team,

Is there a way to see the ASV and their associated fastq files? Is there a output from QIIME2 for this? Currently, my output files are sample-metadata.tsv, table.qzv, table.tsv, taxomomy.qzv, table.qza, rep-seqs.qza, taxa-bar-plots.qzv. We need the actual DNA sequence for each ASV so that they can be aligned with a phylogenetic tree generated.


Hi @Huiyun_Wu,

The rep-seqs.qza file contains your sequences. Check out the exporting tutorial to see how you can get this into a fasta file.



It should be in your rep-seqs.qza file. You can open it as an archive or extract it by exporting command:

qiime tools export \
    --input-path rep-seqs.qza \
    --output-path Rep-seqs/
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