Question

Align pacbio subreads against assembled pacbio reads

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3.4 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 • 1.1k views

ADD COMMENT • link updated 3.4 years ago by Istvan Albert 100k • written 3.4 years ago by wes ▴ 90

score 1 · Answer 1 · 2020-11-18

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3.4 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 3.4 years ago by lieven.sterck 15k

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Thanks for the suggestion!

ADD REPLY • link 3.4 years ago by wes ▴ 90

score 1 · Answer 2 · 2020-11-18

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3.4 years ago

Istvan Albert 100k

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

ADD COMMENT • link 3.4 years ago by Istvan Albert 100k

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whoops lieven.sterck beat me to it

ADD REPLY • link 3.4 years ago by Istvan Albert 100k

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no worries, I'll respect hierarchy ;-)

ADD REPLY • link 3.4 years ago by lieven.sterck 15k

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Thanks for the recommendation!

ADD REPLY • link 3.4 years ago by wes ▴ 90