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  • karinlag
    started a topic undertanding quast output

    undertanding quast output

    I am running quast to evaluate my asms, but I am having trouble understanding the output.

    Here is an example:

    ll statistics are based on contigs of size >= 500 bp, unless otherwise noted (e.g., "# contigs (>= 0 bp)" and "Total length (>= 0 bp)" include all contigs).

    Assembly scaffolds
    # contigs (>= 0 bp) 915
    # contigs (>= 1000 bp) 155
    Total length (>= 0 bp) 4913353
    Total length (>= 1000 bp) 4784814
    # contigs 210
    Largest contig 220067
    Total length 4823052
    GC (%) 50.76
    N50 89965
    N75 37748
    L50 19
    L75 41
    # N's per 100 kbp 26.35


    I could not understand from the manual what the # contigs _without_ any other qualifications mean. Anybody know?

    And, why does it say scaffolds on top?

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