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  • SSPACE creates tandem duplications instead of merging

    Hi all,

    I'm using SSPACE v2.0 on a set of contigs assembled through Velvet, with parameters
    -x = 0
    -z = 0
    -k = 5
    -a = 0.7
    -n = 15
    -p = 0

    Reads library is a 400bp insert PE illumina 2x90bp.

    But when connecting overlapping contigs, the soft scaffolds them with a 'N' spacing instead of merging them. Such an issue should have been corrected in the current version of SSPACE ( see http://seqanswers.com/forums/showpos...3&postcount=97 ), but it does not work for me. Moreover, some overlaps are below 50 bp, i.e. the before-correction threshold.

    Perhaps it may help, but all cases I checked for show multiple link possibilities.

    Did it happened to anyone else with SSPACE v2.0 ?

    thanks,

    seb.

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