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Align multiple Illumina PE reads at once using minimap2?

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

alignment sequencing minimap2
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written by barvazduck • barvazduck

1 answer

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

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written by lieven.sterck lieven.sterck

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