Unique sequences in Qiime

Dear all,
I’m interesting in analyzing the unique sequences found in fasta file that indicates sequences that are identical to the reference sequence. How could I extract the unique sequences?

Thank you!

Hi @teleos,
Assuming that your fasta consists of unique sequences (ASVs or OTUs) output from one of the denoising/dereplication/otu picking methods in QIIME2, you can extract sequences that are identical to reference sequences by using exclude-seqs. Just set the --p-perc-identity parameter to 1.0 to extract exact matches.

I hope that helps!

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Hi @Nicholas_Bokulich,

Thanks for your response. Yes that helps great thanks! I’ll give it a try.

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