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  • marct
    Member
    • Oct 2013
    • 11
    #1

    re-scaffolding using BAC end read pairs

    Hello,

    I have a vertebrate genome assembly with contigs and scaffolds generated from ~80X PE Illumina small-insert and mate-pair libraries. There are also some BAC scaffolds and a few thousand BAC Sanger reads available for this species in the GenBank Trace database. I would like to use these publicly available data to merge scaffolds and improve on the Illumina-only assembly.

    Aligning the assembled BAC scaffolds to the original genome scaffolds and generating consensus sequences to merge contigs/scaffolds seems fairly straightforward, can anyone recommend a method/pipeline that has worked for them? This was mentioned once here http://seqanswers.com/forums/showthr...ght=sspace+bac

    I assume I can use the BAC end paired sequences with a scaffolding tool such as SSPACE (http://seqanswers.com/forums/showpos...6&postcount=11 ) but what is the best way to trim or at least incorporate quality scores? I don't think I want to simply use the raw traces downloaded from GenBank, unless anyone can convince me otherwise.


    Thanks!
    Tags: bac, bac scaffold, scaffolding, sspace
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