[wgs-assembler-users] Bimodal mate pair library, can I use denovo classification?

[Ole K. T. <o.k...@bi...>]

Hi,
I have a bimodal mate pair library with one peak around 3kbp and the
largest and real peak at 19kbp. When I include this in the assembly,
the scaffolding take ages and the result is not that good (larger than
biological probable scaffolds). If I don't include it, scaffold is
quite quick, but the assembly is a bit more fragmented that with it
included. Without I get around 20000 scaffolds, and I get 7000
scaffolds with it included (around 7000 with Newbler too, which
handles this kinds of library better than CA I think). So I would
rather like to include the library.

classifyMates does not seem to be able to find innie oriented mates,
only outtie PE mates as far as I can see. Could I get around this in a
way? Pretend that the library is outtie, and search for outtie mates
with seperation up to 5kbp or something?

Thank you.

Ole