Producing the Reverse-complement of each sequence in fastq files

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Hi!
I have forward fastq files and I would like to generate the reverse-complement. Is there a way to do this in qiime2?

Thank you

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Hi @teleos! QIIME 2 does not currently have an action for reverse-complementing FASTQ files. We have an open issue tracking this feature, but it’s unclear whether it will be included in QIIME 2 – see the discussion in that thread for details, in particular @gregcaporaso’s comment about potential issues with quality scores and downstream analyses.

If you determine that you need to reverse complement your FASTQ files, I’d suggest using an external tool to accomplish that, and then import the sequences into QIIME 2 to continue analyses.

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