This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Align pacbio subreads against assembled pacbio reads

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
• 1,764 views • link
updated by Istvan Albert Istvan Albert • written by wes • wes

2 answers

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 :) )

• 0 views • link
written by lieven.sterck lieven.sterck

Thanks for the suggestion!

• 0 views • link
written by wes • wes

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

• 0 views • link
written by Istvan Albert Istvan Albert

no worries, I'll respect hierarchy ;-)

• 0 views • link
written by lieven.sterck lieven.sterck

Thanks for the recommendation!

• 0 views • link
written by wes • wes

Log in to answer this question.

More posts like this