Question: Refining of a draft genome with BAC-ends
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gravatar for massimiliano.babbucci
3.7 years ago by
massimiliano.babbucci10 wrote:

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

mapping bac assembly genome • 749 views
ADD COMMENTlink modified 3.7 years ago by h.mon31k • written 3.7 years ago by massimiliano.babbucci10
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gravatar for h.mon
3.7 years ago by
h.mon31k
Brazil
h.mon31k wrote:

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.

ADD COMMENTlink written 3.7 years ago by h.mon31k
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