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Old 10-14-2015, 11:31 AM   #3
Location: Uppsala, Sweden

Join Date: Nov 2010
Posts: 27

We've noticed single-base deletions in PacBio assemblies, via alignment of Illumina reads to otherwise very nice Pacbio assemblies. These occur about every 10^3 to 10^4 bases, and we've also found them to be connected with even quite short homopolymers.

I wrote a little two-stage script to correct these given the BAM of illumina alignments, you can find out more at its repository (below). As Brian writes I'm sure there are other solutions as well.

Last edited by dgscofield; 10-14-2015 at 11:34 AM.
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