zzh
/
fast-bwa
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Updated release notes

This commit is contained in:
Heng Li 2014-05-15 11:48:28 -04:00
parent 8d2986ece2
commit 012d54fc49
2 changed files with 20 additions and 16 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

34
NEWS
View File

@ -1,8 +1,9 @@
Release 0.7.9 (11 May, 2014) Release 0.7.9 (11 May, 2014)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
This release brings several major changes to BWA-MEM. Notably, BWA-MEM This release brings several major changes to BWA-MEM. Notably, BWA-MEM now
now formally supports PacBio reads. It generally runs faster at a minor cost of 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 accuracy. The speedup is more significant when GRCh38 is in use. More
specifically: specifically:
@ -12,16 +13,16 @@ specifically:
new heuristics to improve PacBio alignment. These changes are not used by new heuristics to improve PacBio alignment. These changes are not used by
default. Users need to add option "-x pacbio" to enable the feature. default. Users need to add option "-x pacbio" to enable the feature.
* Support PacBio subread-to-subread alignment. The feature is enabled with * Support PacBio subread-to-subread alignment (EXPERIMENTAL). This feature is
option "-x pbread". In this mode, the output only gives the overlapping enabled with option "-x pbread". In this mode, the output only gives the
region between a pair of reads without detailed alignment. 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. * Output alternative hits in the XA tag if there are not so many of them. This
This feature is originally implemented in BWA-backtrack. is a BWA-backtrack feature.
* EXPERIMENTAL feature to support mapping to ALT contigs in GRCh38. We prodive * Support mapping to ALT contigs in GRCh38 (EXPERIMENTAL). We provide a script
a script to postprocess hits in the XA tag to adjust the mapping quality and to postprocess hits in the XA tag to adjust the mapping quality and generate
generate new primary alignments to all overlapping ALT contigs. We would NOT new primary alignments to all overlapping ALT contigs. We would NOT
recommended this feature for production uses. recommended this feature for production uses.
* Improved alignments to many short reference sequences. Older BWA-MEM may * 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 * 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 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 lower the mapping quality if a read contains seeds with excessive
occurrences. These changes make BWA-MEM XXX faster for mapping short reads occurrences. These changes make BWA-MEM faster at a minor cost of accuracy
to GRCh37 and XXX faster to GRCh38. in highly repetitive regions.
* Added an option "-Y" to use soft clipping for supplementary alignments. * 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: 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) (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. read man page for more information about this software.
(0.1.1: 03 June 2008, r349) (0.1.1: 03 June 2008, r349)

2
README.md
View File

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