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Old 10-12-2015, 10:40 AM   #2
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

Illumina does not usually have problems with indels, homopolymer or not. PacBio has a high indel rate in the raw reads and homopolymers are harder to correct, particularly if you don't have enough coverage. You might run quiver to attempt to correct these errors. There are also other programs for correcting assemblies via alignment (ideally using Illumina reads as they generally lack indel errors), but I don't know which is best.
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