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r304: prepare release notes (not released yet)

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Heng Li 2013-02-27 16:55:07 -05:00
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Beta Release 0.7.0 (28 Feburary, 2013)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
This release comes with a new alignment algorithm, BWA-MEM, for 70bp-1Mbp query
sequences. BWA-MEM essentially seeds alignments with a variant of the fastmap
algorithm and extends seeds with banded affine-gap-penalty dynamic programming
(i.e. the Smith-Waterman-Gotoh algorithm). For typical Illumina 100bp reads or
longer low-divergence query sequences, BWA-MEM is about twice as fast as BWA
and BWA-SW and is more accurate. It also supports split alignments like BWA-SW
and may optionally output multiple hits like BWA. BWA-MEM does not guarantee
to find hits within a certain edit distance, but BWA is not efficient for such
task given longer reads, either, and the edit-distance criterion is arguably
not as important in long-read alignment.
In addition to the algorithmic improvements, BWA-SW also implements a few
handy features, some of which are experimental:
1. BWA-MEM automatically infers pair orientation from a batch of single-end
alignments. It allows more than one orientations if there are sufficient
reads supporting them. This feature has not been tested on reads from
Illumina jumping library yet.
2. BWA-MEM optionally takes one interleaved fastq for paired-end mapping. It
is possible to convert a name-sorted BAM to an interleaved fastq on the fly
and feed the data stream to BWA-MEM for mapping.
3. BWA-MEM optionally copies FASTA/Q comments to the final SAM output. This
helps to transfer individual read annotations to the output.
4. BWA-MEM supports more advanced piping. Users can now run:
(bwa mem ref.fa '<bzcat r1.fq.bz2' '<bzcat r2.fq.bz2') to map bzip'd read
files without replying on the bash feature.
The BWA-MEM algorithm is in the beta phase. It is not advised to use BWA-MEM
for production use yet. However, when the implementation becomes stable after a
few release cycles, existing BWA users are recommended to migrate to BWA-MEM
for 76bp or longer Illumina reads and long query sequences. The original BWA
short-read algorithm will not deliver satisfactory results for 150bp+ Illumina
reads. Change of mappers will be necessary sooner or later.
(0.7.0 beta: 28 Feburary 2013, r304)
Release 0.6.2 (19 June, 2012)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~