Minimap2: Align multiple illumina PE reads at once with minimap2

[xbarvazx]

Hi,

How can I align multiple Illumina PE reads at once using minimap2?

I tried something like this:
minimap2 -x sr *_1.fq.gz *_2.fq.gz | gzip > prefix.paf.gz

But it did not work.

Thanks,
Raz

[tseemann]

@xbarvazx you can use subshells in bash like this:

minimap2 -x sr ref.fa <(zcat *_1.fq.gz) <(zcat *_2.fq.gz)