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  • smoics
    Member
    • Jan 2016
    • 15
    #1

    post de novo assembly reference mapping?

    I am curious if there is a program/app that would do post de novo assembly reference mapping--essentially breaking down the full scaffold into chunks and reference mapping it post-assembly.

    I do recognize that I could alternatively use a software to reference map while doing the initial assembly. Just exploring options.
    Tags: bioinformatics sequencing, de novo assembly, reference mapping
  • SNPsaurus
    Registered Vendor
    • May 2013
    • 525
    #2
    The bbtools program shred.sh will break a reference into chunks which can then be used for alignment. I'm not totally sure that is what you are looking for but it is my best bet!
    Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

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