Question: Align pacbio subreads against assembled pacbio reads
0
gravatar for wes
11 days ago by
wes20
wes20 wrote:

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 • 61 views
ADD COMMENTlink modified 11 days ago by Istvan Albert ♦♦ 85k • written 11 days ago by wes20
1
gravatar for lieven.sterck
11 days ago by
lieven.sterck9.0k
VIB, Ghent, Belgium
lieven.sterck9.0k wrote:

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 COMMENTlink modified 11 days ago • written 11 days ago by lieven.sterck9.0k

Thanks for the suggestion!

ADD REPLYlink written 11 days ago by wes20
1
gravatar for Istvan Albert
11 days ago by
Istvan Albert ♦♦ 85k
University Park, USA
Istvan Albert ♦♦ 85k wrote:

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

ADD COMMENTlink written 11 days ago by Istvan Albert ♦♦ 85k

whoops lieven.sterck beat me to it

ADD REPLYlink written 11 days ago by Istvan Albert ♦♦ 85k

no worries, I'll respect hierarchy ;-)

ADD REPLYlink written 11 days ago by lieven.sterck9.0k

Thanks for the recommendation!

ADD REPLYlink written 11 days ago by wes20
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