bwa/bwa-0.7.17/NEWS.md

53 minor features. All BWA algorithms should produce identical output to 0.7.12
71    license. This allows us to create an Apache2-licensed BWA (in the "Apache2"
91 A major change to BWA-MEM is the support of mapping to ALT contigs in addition
93 BWA-MEM and the rest in a postprocessing script for now. Due to the extra
97 For general uses, the single BWA binary still works like the old way.
99 Another major addition to BWA-MEM is HLA typing, which made possible with the
104 Other notable changes to BWA-MEM:
114  * Dropped PacBio read-to-read alignment for now. BWA-MEM is good for finding
153 Notable changes to BWA-MEM:
172 This release brings several major changes to BWA-MEM. Notably, BWA-MEM now
174 PacBio read-to-read alignment. BWA-MEM also runs faster at a minor cost of
178  * Support PacBio subread-to-reference alignment. Although older BWA-MEM works
189    is a BWA-backtrack feature.
196  * Improved alignments to many short reference sequences. Older BWA-MEM may
200    from the very beginning. BWA-MEM should not produce an alignment bridging
206    occurrences. These changes make BWA-MEM faster at a minor cost of accuracy
221 Changes in BWA-backtrack:
233 Changes in BWA-MEM:
265 This release fixes incorrect MD tags in the BWA-MEM output.
270 BWA-MEM -50% slower. If you are concerned with the performance of BWA-MEM, you
282 Changes in BWA-MEM:
322 There are no changes to BWA-backtrack in this release. However, it has a few
323 known issues yet to be fixed. If you prefer BWA-track, It is still advised to
326 While I developed BWA-MEM, I also found a few issues with BWA-SW. It is now
327 possible to improve BWA-SW with the lessons learned from BWA-MEM. However, as
328 BWA-MEM is usually better, I will not improve BWA-SW until I find applications
329 where BWA-SW may excel.
338 Fixed a bug in BWA-backtrack which leads to off-by-one mapping errors in rare
357 Changes in BWA-MEM:
374 Changes in BWA-backtrack:
386 In addition, if you use BWA-MEM or the fastmap command of BWA, please cite:
389    with BWA-MEM. arXiv:1303.3997v2 [q-bio.GN].
412    around tandem repeat. This will lead to a suboptimal CIGAR in BWA-MEM and
413    a wrong CIGAR in BWA.
422 Since version 0.7.4, BWA-MEM is considered to reach similar stability to
423 BWA-backtrack for short-read mapping.
442 Changes to BWA-MEM:
449    reads, and there are no other substitutions or indels. BWA-MEM would not do
456 BWA-MEM has been used to align -300Gbp 100-700bp SE/PE reads. SNP/indel calling
457 has also been evaluated on part of these data. BWA-MEM generally gives better
458 pre-filtered SNP calls than BWA. No significant issues have been observed since
463 In addition, more detailed description of the BWA-MEM algorithm can be found at
483 Changes to BWA-MEM:
491    BWA-MEM can now be validated with Picard.
498  * In BWA-backtrack and BWA-SW, replaced the code for global alignment,
506 An important note is that like BWA-SW, BWA-MEM may output multiple primary
519 This release comes with a new alignment algorithm, BWA-MEM, for 70bp-1Mbp query
520 sequences. BWA-MEM essentially seeds alignments with a variant of the fastmap
523 longer low-divergence query sequences, BWA-MEM is about twice as fast as BWA
524 and BWA-SW and is more accurate. It also supports split alignments like BWA-SW
525 and may optionally output multiple hits like BWA. BWA-MEM does not guarantee
526 to find hits within a certain edit distance, but BWA is not efficient for such
530 In addition to the algorithmic improvements, BWA-MEM also implements a few
533  1. BWA-MEM automatically switches between local and glocal (global wrt reads;
538  2. BWA-MEM automatically infers pair orientation from a batch of single-end
543  3. BWA-MEM optionally takes one interleaved fastq for paired-end mapping. It
545     and feed the data stream to BWA-MEM for mapping.
547  4. BWA-MEM optionally copies FASTA/Q comments to the final SAM output, which
550  5. BWA-MEM supports more advanced piping. Users can now run:
554  6. BWA-MEM provides a few basic APIs for single-end mapping. The 'example.c'
558 The BWA-MEM algorithm is in the beta phase. It is not advised to use BWA-MEM
560 few release cycles, existing BWA users are recommended to migrate to BWA-MEM
561 for 76bp or longer Illumina reads and long query sequences. The original BWA
572 This is largely a bug-fix release. Notable changes in BWA-short and BWA-SW:
574  * Bugfix: BWA-SW may give bad alignments due to incorrect band width.
582  * Added options '-I' and '-S' to control BWA-SW pairing.
591 Notable changes to BWA-short:
600 Notable changes to BWA-SW:
629 BWA-short by about 20% and BWA-SW by 90% with the mapping acccuracy largely
630 unchanged. A tradeoff is BWA requires more memory, but this is the price almost
633 Secondly, BWA-SW in 0.6.0 now works with paired-end data. It is more accurate
635 variations. However, BWA-short still has edges for reads with many suboptimal
647  * Output the timing information before BWA exits. This also tells users that
664 BWA-SW may be better when reads continue to go longer. I would encourage users
688 Also, since January 13, the BWA master repository has been moved to github:
855 Notable changes in dBWT-SW/BWA-SW:
857  * Changed name dBWT-SW to BWA-SW.
941 Other notable changes in BWA are:
1011 process. Please note that like MAQ, BWA cannot make use of the primer
1108 for BWA and this release seems to be. For paired end reads, BWA also
1110 mapped confidently. With this strategy BWA achieves similar accuracy to
1188  * More clearly define what alignments can be found by BWA (See
1189    manual). Now BWA runs a little slower because it will visit more
1220 This is the first release of BWA, Burrows-Wheeler Alignment tool. Please