hybrid assembly Illumina/454

[Robby]

Hello everyone,
we sequenced an genome with Illumina HiSeq (100bp pe) and 454. In a first step we assembled the Illumina reads with Velvet and would now like to combine the contigs with the 454 reads. Our longest contigs are around 50kb. Unfortunally Mira accepts reads just up to 15kb and Celera just up to 2kb. Which appoaches do you use for hybrid assemblies?

Furthermore we tried use the paired end information for the contig orientation. We are pretty sure, that some contigs overlap at the end. Does anyone know a programm, which allows me to merge two specific contigs?

Thanks a lot
Robby

[nickloman]

I recently wrote a blog post which outlined some strategies for 454 & Illumina hybrid assemblies which you might find useful:

http://pathogenomics.bham.ac.uk/blog/2011/08/assembling-illumina-and-454-data/