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  • A question about definition of "seed" in bwa and bowtie

    As topic ,my question about definition of "seed" in bwa and bowtie , because it can be adjust in parameters.


    If every one know please let me know! thaks!
    Best regard!

  • #2
    from the bowtie manual : http://bowtie-bio.sourceforge.net/manual.shtml

    -n/--seedmms <int> : Maximum number of mismatches permitted in the "seed", i.e. the first L base pairs of the read (where L is set with -l/--seedlen). This may be 0, 1, 2 or 3 and the default is 2. This option is mutually exclusive with the -v option.

    -l/--seedlen <int> : The "seed length"; i.e., the number of bases on the high-quality end of the read to which the -n ceiling applies. The lowest permitted setting is 5 and the default is 28. bowtie is faster for larger values of -l.

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