Fwd: [Bowtie-bio-announce] Bowtie 2 2.0.0-beta4 released

Bowtie 2 2.0.0-beta4 released - 12/6/2011
  * Accuracy improvements.
  * Speed improvements in some situations.
  * Fixed a handful of crashing bugs.
  * Fixed some documentation bugs.
  * Fixed bug whereby --version worked incorrectly.
  * Fixed formatting bug with MD:Z optional field that would sometimes fail to
    follow a mismatch with a number.
  * Added -D option for controlling the maximum number of seed extensions that
    can fail in a row before we move on.  This option or something like it
        will eventually replace the argument to -M.
  * Added -R option to control maximum number of times re-seeding is attempted
    for a read with repetitive seeds.
  * Changed default to --no-dovetail.  Specifying --dovetail turns it back on.
  * Added second argument for --mp option so that user can set maximum and
    minimum mismatch penalties at once.  Also tweaked the formula for
    calculating the quality-aware mismatch penalty.

Bowtie2 website: http://bowtie-bio.sourceforge.net/bowtie2

Thanks,
Ben
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