Sequence format convert


I have forward and reverse fastq data that was imported into qiime2 as paired-end sequences with quality. How am I able to convert the sequence into SampleData[JoinedSequencesWithQuality] | SampleData[SequencesWithQuality] | SampleData[Sequences] that can be used for qiime vsearch dereplicate-sequences

Thanks for your help
Bowen Zhang

Hi @zhang_sonic,

I think what you are looking for is vsearch join-pairs. I’ll also add, in case you aren’t aware already, unless you specifically need to do OTU clustering methods for some reason there are better methods available in qiime2 such as DADA2 and Deblur for denoising your reads and avoids arbitrary % identity clustering methods such as those in vsearch. For DADA2, it will also merge the reads on its own so you wouldn’t need to do this yourself prior.

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