Assembling Paralogs

[park6728]

Hello,
I was wondering if anyone knew of any software/scripts that effectively assemble paralogous copies of individual loci from short read sequence pools. We're specifically working on assembling these from genomic DNA libraries sequenced on Illumina platforms (typically 80-100bp PE), but it doesn't seem like this challenge should really be platform-specific, at least not beyond issues of read length.

In addition, we have loci of interest that share common sequence (say ca. 70bp), but are otherwise highly divergent. This type of situation seems to be giving our assemblers (yasra and price) some fits right now. I would think that this could also be solved in a similar manner as would be done for assembling paralogous loci, and perhaps could be approached using RNAseq software that is effective at assembling isoforms(?).

Thanks, any thoughts would be appreciated!

[Wallysb01]

I think what you might want to try is ABySS. Usually ABySS is used for whole genome or whole transcriptome assembly, but if you're interested in targeted assembly, I'm not that should matter.

Another option is velvet, which is pretty memory intensive, but if your region of interest is small it might be able to run on something with 64 GB of RAM.