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jordangumm / metago

Experimental metagenomic workflow
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QC for fastq read pairs in assembly #1

Open morglind opened 6 years ago

morglind commented 6 years ago

Can we add a QC step that verifies there is the same number of forward and reverse reads?

jordangumm commented 6 years ago

Totally! QC should definitely catch issues like this.

jordangumm commented 6 years ago

Commit 19f4edea771553196f227475ea03c54d48e46160 should "fix" this.

It's a heuristic, as it just assumes that the forward and reverse strand files should be relatively the same size. A full check would be relatively time consuming. Also, I would think that all successfully bcl2fastq (assuming illumina only) demultiplexed fastq paired-end files should have the same number of forward and reverse strand reads.

jordangumm commented 6 years ago

Although, maybe we should add an option in the cli to perform this task.