Estimate insert size for pacbio long reads

Question

[arunprasanna83]

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.

[jean.elbers]

You should probably use PBJelly (https://sourceforge.net/p/pb-jelly/wiki/Home/). 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 CallVariants.sh) did a better job in terms of BUSCO scores and RNA-Seq mapping rates than running Pilon.