Creating manifest file for fastq files that contain both forward and reverse reads

[colinbrislawn (Colin J Brislawn)]

Hello Kristin,

Great question!

@kristiny

My .fastq files contain both forward and reverse reads in the same file.

Based on this answer, it looks like interleaved fastq files are not supported quite yet.

How do I import interleaved fastq files?

Thanks so much for all that information! I've created an issue to track this format. This corresponds to extract_reads_from_interleaved_file.py in QIIME 1, so there's a fair chance we'll have this in the next few months as we work towards feature-parity with QIIME 1.

That issue is still open

Let's see if the Qiime developers can suggest a workaround.

Colin