[wgs-assembler-users] Assembling with both Illum and PacBio

[Powers, J. <jp...@ex...>]

Hi all,

Trying to do a hybrid assembly with PacBio and Illum short reads. Essentially this is what I am trying to do: Correct PacBio with Illumina. Assembly Corrected PacBio reads with about 5X of Illumina reads. The reason I want to add in the paired end Illumina reads is that at the end of the assembly, I would like to use amosvalidate to evaluate assembly-correctness. While you can do amosvalidate without paired end reads, it is more powerful if you can incorporate that data, so I thought by sprinkling in a low amount of Illumina reads into the assembly, I could take advantage of this. Unfortunately assembly using both consistently fails during the overlap phase. Sometimes it gets to 1-overlapper, sometimes it fails on  0-overlaptrim-overlap. But it just doesn't want to finish.  I've encountered overlap failures before, and found that some nodes in the cluster I am using that seem to have problems with the installation/dependencies. However tracking the nodes here, it seems pretty scattershot.

Any thoughts on what might be happening, or alternatively, how I can assemble the pacbio reads and add in Illumina reads post-assembly for use with amosvalidate?


Thanks,
Jason