[maq-announce] Release bwa-0.5.1

[Heng Li <lh...@sa...>]

Hello,

I have set up a new SourceForge Project for BWA as several people are
complaining the coexistence of maq and bwa is confusing. The new BWA
homepage is at:

http://bio-bwa.sourceforge.net/

BWA source codes have been put in the SVN for that project. Bugs and
feature requests can still be sent to the maq-help mailing list.

Heng


Beta Release 0.5.1 (2 September, 2009)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Notable changes in the short read alignment component:

 * Fixed a bug in samse: do not write mate coordinates.

Notable changes in dBWT-SW:

 * Randomly choose one alignment if the read is a repetitive.

 * Fixed a flaw when a read is mapped across two adjacent reference
   sequences. However, wrong alignment reports may still occur rarely in
   this case.

 * Changed the default band width to 50. The speed is slower due to this
   change.

 * Improved the mapping quality a little given long query sequences.

(0.5.1: 2 September 2009, r1209)



Beta Release 0.5.0 (20 August, 2009)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

This release implements a novel algorithm, dBWT-SW, specifically
designed for long reads. It is 10-50 times faster than SSAHA2, depending
on the characteristics of the input data, and achieves comparable
alignment accuracy while allowing chimera detection. In comparison to
BLAT, dBWT-SW is several times faster and much more accurate especially
when the error rate is high. Please read the manual page for more
information.

The dBWT-SW algorithm is kind of developed for future sequencing
technologies which produce much longer reads with a little higher error
rate. It is still at its early development stage. Some features are
missing and it may be buggy although I have evaluated on several
simulated and real data sets. But following the "release early"
paradigm, I would like the users to try it first.

Other notable changes in BWA are:

 * Fixed a rare bug in the Smith-Waterman alignment module.

 * Fixed a rare bug about the wrong alignment coordinate when a read is
   poorly aligned.

 * Fixed a bug in generating the "mate-unmap" SAM tag when both ends in
   a pair are unmapped.

(0.5.0: 20 August 2009, r1200)



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