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jdidion / atropos

An NGS read trimming tool that is specific, sensitive, and speedy. (production)
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Trimmed fastq ordering is not deterministic #106

Closed annamerk closed 4 years ago

annamerk commented 4 years ago

Running atropos multiple times produces fastqs with different read orders. It would be great if the ordering was deterministic.

atropos --threads 8 $ADAPTERS -o r1.trimmed.fastq.gz -p r2.trimmed.fastq.gz -pe1 r1.fastq.gz -pe2 r2.fastq.gz

Otherwise is there a recommended performant way to sort the outputs?

jdidion commented 4 years ago

This is what the —preserve-order option is for.

annamerk commented 4 years ago

Oh, I missed that one. Thanks for the quick response!