Align pacbio subreads against assembled pacbio reads
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7 months ago
wes ▴ 50

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 • 208 views
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7 months ago

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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Thanks for the suggestion!

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7 months ago

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

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whoops lieven.sterck beat me to it

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no worries, I'll respect hierarchy ;-)

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Thanks for the recommendation!

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