Question: Align multiple Illumina PE reads at once using minimap2?
0
gravatar for barvazduck
12 months ago by
barvazduck10
Israel
barvazduck10 wrote:

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

sequencing alignment minimap2 • 299 views
ADD COMMENTlink written 12 months ago by barvazduck10
1
gravatar for lieven.sterck
12 months ago by
lieven.sterck8.0k
VIB, Ghent, Belgium
lieven.sterck8.0k wrote:

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

ADD COMMENTlink modified 12 months ago • written 12 months ago by lieven.sterck8.0k

Right! Thanks,

Raz

ADD REPLYlink written 12 months ago by barvazduck10
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