Refining of a draft genome with BAC-ends
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
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h.mon
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massimiliano.babbucci •
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massimiliano.babbucci •
1 answer
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.
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