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  • Velvet assembler ambiguous calls

    Hello,

    I'm using Velvet assembler and I've a little doubt.
    After reading Velvet documentation I know that one gap in output assembly is represented by minimum of 10 N's. And that the number of N's represent the estimated gap length.

    However I can't find information about how does Velvet treat ambiguous calls. I would like to know how Velvet represents the ambiguous calls in output contigs.fa

    Does Velvet replace ambiguous calls with a random nucleotide (A, C, T or G)?

    Thank you very much.
    Last edited by gmarco; 06-23-2014, 12:21 AM.

  • #2
    I've got answer from Daniel Zerbino (creator of Velvet). In case anyone else interested:

    Velvet does not support ambiguous call, it just makes a majority call.
    Last edited by gmarco; 06-23-2014, 06:50 AM.

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