Question

Align pacbio subreads against assembled pacbio reads

2

Entering edit mode

4.0 years ago

wes ▴ 90

I have a fasta file consists of contigs generated using canu with Pacbio long read sequence. Now I would like to align the pacbio subread to these contigs and visualize it using IGV to have an idea how many subread cover a particular region of interest. May I know which software should I use? can pbalign tool use for such purpose?

alignment • 1.2k views

ADD COMMENT • link updated 4.0 years ago by Istvan Albert 102k • written 4.0 years ago by wes ▴ 90

score 1 · Answer 1 · 2020-11-18

1

Entering edit mode

4.0 years ago

lieven.sterck 15k

pbalign can do this indeed.

personally I would go for something like minimap(2) or such. much faster and at least as accurate (PBalign is a pita, again personal opinion :) )

ADD COMMENT • link 4.0 years ago by lieven.sterck 15k

0

Entering edit mode

Thanks for the suggestion!

ADD REPLY • link 4.0 years ago by wes ▴ 90

score 1 · Answer 2 · 2020-11-18

1

Entering edit mode

4.0 years ago

Istvan Albert 102k

I would recommend minimap2, it has modes for pacbio as well.

ADD COMMENT • link 4.0 years ago by Istvan Albert 102k

0

Entering edit mode

whoops lieven.sterck beat me to it

ADD REPLY • link 4.0 years ago by Istvan Albert 102k

0

Entering edit mode

no worries, I'll respect hierarchy ;-)

ADD REPLY • link 4.0 years ago by lieven.sterck 15k

0

Entering edit mode

Thanks for the recommendation!

ADD REPLY • link 4.0 years ago by wes ▴ 90