Export merged paired-end fastq files

I need to merge demultiplexed paired-end reads to a single fastq file for each sample for uploading to a repository. Is there a way to obtain these files from QIIME2, rather than using a completely separate tool like FLASh?

I checked the demux-paired-end.qza file and there is still a R1 and R2 file for every sample, so I assume that they aren’t merged?

Thanks in advance!


Hi, @kms285! Welcome to the forum. :smiley:

If I understand correctly, the following workflow should get you what you need:

First, use the join-pairs method to merge your paired-end data:

qiime vsearch join-pairs \
  --i-demultiplexed-seqs demux.qza \
  --o-joined-sequences joined.qza

This will generate an SampleData[JoinedSequencesWithQuality] artifact, which you can then export:

 qiime tools export \
  --input-path joined.qza \
  --output-path joined_fastqs

If you take a look in the resulting directory you will find a single fastq for each of your samples.

1 Like

This worked perfectly! Thank you!