Align multiple Illumina PE reads at once using minimap2?

Question

[barvazduck]

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

Answer 1

[lieven.sterck]

Any specific reason why you want to use minimap to do this? minimap is an aligner for 'long' reads where you have short reads (illumina).

I would suggest to use tools like HiSat2, STAR, BBmap ,... to align illumina PE reads

[barvazduck]

Right! Thanks,

Raz