hybrid assembly for PacBio and Illumina data

[laelaps]

I am working on a project in which we have sequence data on the same regions and individuals from Pacific Biosciences and Illumina. The PacBio reads are much longer (around 2400 bp) but the Illumina reads (only 100 bp long) are of higher quality. We are interested in doing de novo assembly with the PacBio reads to build a scaffold and then would like to map the Illumina reads to it.

There was a prior post on this but it is from mid-2009. http://seqanswers.com/forums/showthread.php?t=10401

What are the current methods to do this kind of hybrid assembly? What methods have been found to work particularly well?

[tplsmith]

The new v1.3 release from PacBio supposedly supports hybrid assembly, I have not made much attempt to get it to work since we had already implemented a pipeline based on the PacBioToCA plug-in for the Celera Assembler that was written by Sergey Koren at NBACC. This script uses short read, high quality data to error correct the PacBio reads and outputs a .frg file suitable for OLC assembly in CA. We have been able to create single-contig chromosomes of bacteria with no finishing steps using this approach, for several different species. Some species with very large repetitive phage integrations are more difficult if you need to know exactly which slight variants of these are in which chromosomal position.