Question: Estimate insert size for pacbio long reads
gravatar for arunprasanna83
6 months ago by
arunprasanna8330 wrote:

I am trying to use pacbio long reads to do gap filling using GapFiller program. What is the correct way of specifying the insert size mentioned in library file ? In other words, how to estimate insert size for pacbio long reads (SMRT).

Thanks in Advance.

gapfilling next-gen assembly • 287 views
ADD COMMENTlink written 6 months ago by arunprasanna8330

You should probably use PBJelly ( Here are some instructions for running PBJelly for PacBio Sequel subreads and error correcting using a variant caller instead of Pilon to correct indels (. I also have another gist if you want to some instructions to run Pilon (, but I have found that BBTool's variant caller did a better job in terms of BUSCO scores and RNA-Seq mapping rates than running Pilon.

ADD REPLYlink written 6 months ago by jean.elbers1.1k
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