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

[Walenz, B. <bw...@jc...>]

Hi, Jason-

Can you send the spec and at least one of the error files from overlapper?  Is this CA7 (the release) or the CVS version?  I suspect overlapper might be exhausting memory.  The error file reports how much memory it is allocating for the large data structures.

In CA7, Illumina reads must be loaded before long reads, otherwise memory usage is higher than it should be.  In the CVS version, the assembler will check for this problem.

bri


On 7/17/12 12:37 PM, "Powers, Jason" <jp...@ex...> wrote:

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