Refining of a draft genome with BAC-ends

Question

[massimiliano.babbucci]

Dear All, we have a genome draft of about 55000 scaffolds and 99000 BAC-ends for/rev. We would like to use these BAC-ends to refine the genome obtaining super-scaffolds. We also have mapped the BAC sequences against our draft obtaining a SAM file with 22000 contigs linked. Does anybody know any tool or pipeline to do this task? Thanks a lot in advance

Answer 1

[h.mon]

If you can map your BAC-ends, then any scaffolder should work. See this paper for a review. In addition, this thread specifically mentions SSPACE for BAC-ends.

Also, if you are willing to assemble you genome again, Allpaths-LG accepts long jumping libraries (insert greater than 20kb), they are used for scaffolding only.