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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
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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 :) )

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written by lieven.sterck lieven.sterck

Thanks for the suggestion!

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written by wes • wes

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

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written by Istvan Albert Istvan Albert

no worries, I'll respect hierarchy ;-)

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written by lieven.sterck lieven.sterck

Thanks for the recommendation!

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written by wes • wes

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