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  • edge
    Senior Member
    • Sep 2009
    • 199

    #1

    How to assess Phrap assembly result

    Hi,

    Currently I was running Phrap for re-assemble of my transcriptome data-set.
    The command that I run for Phrap is shown as below:
    phrap -minscore 100 -ace assembly.contig.fna

    Can I know how to assess the re-assembly done by Phrap whether is good or bad?
    Initial assembly contig gives 369,546 seq, total bases 301,280,040, N50 is 2,077;
    Phrap re-assembly gives singlets + contigs gives 88,136 + 120,205 = 208,143 seq, total bases 300,282,588, N50 is 2,370;

    Thanks.

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