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Updated release notes

This commit is contained in:
Heng Li 2014-05-15 11:48:28 -04:00
parent 8d2986ece2
commit 012d54fc49
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34
NEWS
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@ -1,8 +1,9 @@
Release 0.7.9 (11 May, 2014)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
This release brings several major changes to BWA-MEM. Notably, BWA-MEM
now formally supports PacBio reads. It generally runs faster at a minor cost of
This release brings several major changes to BWA-MEM. Notably, BWA-MEM now
formally supports PacBio read-to-reference alignment and experimentally support
PacBio read-to-read alignment. BWA-MEM also runs faster at a minor cost of
accuracy. The speedup is more significant when GRCh38 is in use. More
specifically:
@ -12,16 +13,16 @@ specifically:
new heuristics to improve PacBio alignment. These changes are not used by
default. Users need to add option "-x pacbio" to enable the feature.
* Support PacBio subread-to-subread alignment. The feature is enabled with
option "-x pbread". In this mode, the output only gives the overlapping
region between a pair of reads without detailed alignment.
* Support PacBio subread-to-subread alignment (EXPERIMENTAL). This feature is
enabled with option "-x pbread". In this mode, the output only gives the
overlapping region between a pair of reads without detailed alignment.
* Output alternative hits in the XA tag if there are not so many such hits.
This feature is originally implemented in BWA-backtrack.
* Output alternative hits in the XA tag if there are not so many of them. This
is a BWA-backtrack feature.
* EXPERIMENTAL feature to support mapping to ALT contigs in GRCh38. We prodive
a script to postprocess hits in the XA tag to adjust the mapping quality and
generate new primary alignments to all overlapping ALT contigs. We would NOT
* Support mapping to ALT contigs in GRCh38 (EXPERIMENTAL). We provide a script
to postprocess hits in the XA tag to adjust the mapping quality and generate
new primary alignments to all overlapping ALT contigs. We would NOT
recommended this feature for production uses.
* Improved alignments to many short reference sequences. Older BWA-MEM may
@ -34,8 +35,8 @@ specifically:
* Reduced the maximum seed occurrence from 10000 to 500. Reduced the maximum
number of Smith-Waterman mate rescue from 100 to 50. Added a heuristic to
lower the mapping quality if a read contains seeds with excessive
occurrences. These changes make BWA-MEM XXX faster for mapping short reads
to GRCh37 and XXX faster to GRCh38.
occurrences. These changes make BWA-MEM faster at a minor cost of accuracy
in highly repetitive regions.
* Added an option "-Y" to use soft clipping for supplementary alignments.
@ -43,6 +44,12 @@ specifically:
* Bugfix: integer overflow when aligning low query sequences.
* Bugfix: chain score is not computed correctly (almost no practical effect)
* General code cleanup
* Added FAQs to README
(0.7.9: 11 May 2014, r777)
@ -1041,6 +1048,3 @@ This is the first release of BWA, Burrows-Wheeler Alignment tool. Please
read man page for more information about this software.
(0.1.1: 03 June 2008, r349)

2
README.md
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@ -24,7 +24,7 @@ different sub-commands: **aln/samse/sampe** for BWA-backtrack,
##Availability
BWA is released under [GPLv3][1]. The latest souce code is [freely
BWA is released under [GPLv3][1]. The latest source code is [freely
available at github][2]. Released packages can [be downloaded][3] at
SourceForge. After you acquire the source code, simply use `make` to compile
and copy the single executable `bwa` to the destination you want. The only