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  • RLB_84
    Junior Member
    • Nov 2010
    • 4
    #1

    Alternate contig scaffoldings with ABySS

    Hi everybody,
    I would like to know if anyone tried to scaffold contigs returned from ABYSS using several n (the minimum number of pairs needed to consider joining two contigs) values, starting from the same dataset of contigs obtained with a certain k value. How should I run the abyss-pe script in order to start from ABYSS results (*-3.fa, lib.hist and lib.dist) and not to perform the assembly again?

    I use Abyss 1.2.5. I run it on a Mac machine and encountered some difficulties in compiling 1.3.0.

    Thanks to everybody
    Tags: abyss, abyss-pe, de novo assembly, scaffolding
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