|
0
|
1 Beta Release 0.5.7 (1 March, 2010)
|
|
|
2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
3
|
|
|
4 This release only has an effect on paired-end data with fat insert-size
|
|
|
5 distribution. Users are still recommended to update as the new release
|
|
|
6 improves the robustness to poor data.
|
|
|
7
|
|
|
8 * The fix for `weird pairing' was not working in version 0.5.6, pointed
|
|
|
9 out by Carol Scott. It should work now.
|
|
|
10
|
|
|
11 * Optionally output to a normal file rather than to stdout (by Tim
|
|
|
12 Fennel).
|
|
|
13
|
|
|
14 (0.5.7: 1 March 2010, r1310)
|
|
|
15
|
|
|
16
|
|
|
17
|
|
|
18 Beta Release 0.5.6 (10 Feburary, 2010)
|
|
|
19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
20
|
|
|
21 Notable changes in bwa-short:
|
|
|
22
|
|
|
23 * Report multiple hits in the SAM format at a new tag XA encoded as:
|
|
|
24 (chr,pos,CIGAR,NM;)*. By default, if a paired or single-end read has
|
|
|
25 4 or fewer hits, they will all be reported; if a read in a anomalous
|
|
|
26 pair has 11 or fewer hits, all of them will be reported.
|
|
|
27
|
|
|
28 * Perform Smith-Waterman alignment also for anomalous read pairs when
|
|
|
29 both ends have quality higher than 17. This reduces false positives
|
|
|
30 for some SV discovery algorithms.
|
|
|
31
|
|
|
32 * Do not report "weird pairing" when the insert size distribution is
|
|
|
33 too fat or has a mean close to zero.
|
|
|
34
|
|
|
35 * If a read is bridging two adjacent chromsomes, flag it as unmapped.
|
|
|
36
|
|
|
37 * Fixed a small but long existing memory leak in paired-end mapping.
|
|
|
38
|
|
|
39 * Multiple bug fixes in SOLiD mapping: a) quality "-1" can be correctly
|
|
|
40 parsed by solid2fastq.pl; b) truncated quality string is resolved; c)
|
|
|
41 SOLiD read mapped to the reverse strand is complemented.
|
|
|
42
|
|
|
43 * Bwa now calculates skewness and kurtosis of the insert size
|
|
|
44 distribution.
|
|
|
45
|
|
|
46 * Deploy a Bayesian method to estimate the maximum distance for a read
|
|
|
47 pair considered to be paired properly. The method is proposed by
|
|
|
48 Gerton Lunter, but bwa only implements a simplified version.
|
|
|
49
|
|
|
50 * Export more functions for Java bindings, by Matt Hanna (See:
|
|
|
51 http://www.broadinstitute.org/gsa/wiki/index.php/Sting_BWA/C_bindings)
|
|
|
52
|
|
|
53 * Abstract bwa CIGAR for further extension, by Rodrigo Goya.
|
|
|
54
|
|
|
55 (0.5.6: 10 Feburary 2010, r1303)
|
|
|
56
|
|
|
57
|
|
|
58
|
|
|
59 Beta Release 0.5.5 (10 November, 2009)
|
|
|
60 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
61
|
|
|
62 This is a bug fix release:
|
|
|
63
|
|
|
64 * Fixed a serious bug/typo in aln which does not occur given short
|
|
|
65 reads, but will lead to segfault for >500bp reads. Of course, the aln
|
|
|
66 command is not recommended for reads longer than 200bp, but this is a
|
|
|
67 bug anyway.
|
|
|
68
|
|
|
69 * Fixed a minor bug/typo which leads to incorrect single-end mapping
|
|
|
70 quality when one end is moved to meet the mate-pair requirement.
|
|
|
71
|
|
|
72 * Fixed a bug in samse for mapping in the color space. This bug is
|
|
|
73 caused by quality filtration added since 0.5.1.
|
|
|
74
|
|
|
75 (0.5.5: 10 November 2009, r1273)
|
|
|
76
|
|
|
77
|
|
|
78
|
|
|
79 Beta Release 0.5.4 (9 October, 2009)
|
|
|
80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
81
|
|
|
82 Since this version, the default seed length used in the "aln" command is
|
|
|
83 changed to 32.
|
|
|
84
|
|
|
85 Notable changes in bwa-short:
|
|
|
86
|
|
|
87 * Added a new tag "XC:i" which gives the length of clipped reads.
|
|
|
88
|
|
|
89 * In sampe, skip alignments in case of a bug in the Smith-Waterman
|
|
|
90 alignment module.
|
|
|
91
|
|
|
92 * In sampe, fixed a bug in pairing when the read sequence is identical
|
|
|
93 to its reverse complement.
|
|
|
94
|
|
|
95 * In sampe, optionally preload the entire FM-index into memory to
|
|
|
96 reduce disk operations.
|
|
|
97
|
|
|
98 Notable changes in dBWT-SW/BWA-SW:
|
|
|
99
|
|
|
100 * Changed name dBWT-SW to BWA-SW.
|
|
|
101
|
|
|
102 * Optionally use "hard clipping" in the SAM output.
|
|
|
103
|
|
|
104 (0.5.4: 9 October 2009, r1245)
|
|
|
105
|
|
|
106
|
|
|
107
|
|
|
108 Beta Release 0.5.3 (15 September, 2009)
|
|
|
109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
110
|
|
|
111 Fixed a critical bug in bwa-short: reads mapped to the reverse strand
|
|
|
112 are not complemented.
|
|
|
113
|
|
|
114 (0.5.3: 15 September 2009, r1225)
|
|
|
115
|
|
|
116
|
|
|
117
|
|
|
118 Beta Release 0.5.2 (13 September, 2009)
|
|
|
119 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
120
|
|
|
121 Notable changes in bwa-short:
|
|
|
122
|
|
|
123 * Optionally trim reads before alignment. See the manual page on `aln
|
|
|
124 -q' for detailed description.
|
|
|
125
|
|
|
126 * Fixed a bug in calculating the NM tag for a gapped alignment.
|
|
|
127
|
|
|
128 * Fixed a bug given a mixture of reads with some longer than the seed
|
|
|
129 length and some shorter.
|
|
|
130
|
|
|
131 * Print SAM header.
|
|
|
132
|
|
|
133 Notable changes in dBWT-SW:
|
|
|
134
|
|
|
135 * Changed the default value of -T to 30. As a result, the accuracy is a
|
|
|
136 little higher for short reads at the cost of speed.
|
|
|
137
|
|
|
138 (0.5.2: 13 September 2009, r1223)
|
|
|
139
|
|
|
140
|
|
|
141
|
|
|
142 Beta Release 0.5.1 (2 September, 2009)
|
|
|
143 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
144
|
|
|
145 Notable changes in the short read alignment component:
|
|
|
146
|
|
|
147 * Fixed a bug in samse: do not write mate coordinates.
|
|
|
148
|
|
|
149 Notable changes in dBWT-SW:
|
|
|
150
|
|
|
151 * Randomly choose one alignment if the read is a repetitive.
|
|
|
152
|
|
|
153 * Fixed a flaw when a read is mapped across two adjacent reference
|
|
|
154 sequences. However, wrong alignment reports may still occur rarely in
|
|
|
155 this case.
|
|
|
156
|
|
|
157 * Changed the default band width to 50. The speed is slower due to this
|
|
|
158 change.
|
|
|
159
|
|
|
160 * Improved the mapping quality a little given long query sequences.
|
|
|
161
|
|
|
162 (0.5.1: 2 September 2009, r1209)
|
|
|
163
|
|
|
164
|
|
|
165
|
|
|
166 Beta Release 0.5.0 (20 August, 2009)
|
|
|
167 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
168
|
|
|
169 This release implements a novel algorithm, dBWT-SW, specifically
|
|
|
170 designed for long reads. It is 10-50 times faster than SSAHA2, depending
|
|
|
171 on the characteristics of the input data, and achieves comparable
|
|
|
172 alignment accuracy while allowing chimera detection. In comparison to
|
|
|
173 BLAT, dBWT-SW is several times faster and much more accurate especially
|
|
|
174 when the error rate is high. Please read the manual page for more
|
|
|
175 information.
|
|
|
176
|
|
|
177 The dBWT-SW algorithm is kind of developed for future sequencing
|
|
|
178 technologies which produce much longer reads with a little higher error
|
|
|
179 rate. It is still at its early development stage. Some features are
|
|
|
180 missing and it may be buggy although I have evaluated on several
|
|
|
181 simulated and real data sets. But following the "release early"
|
|
|
182 paradigm, I would like the users to try it first.
|
|
|
183
|
|
|
184 Other notable changes in BWA are:
|
|
|
185
|
|
|
186 * Fixed a rare bug in the Smith-Waterman alignment module.
|
|
|
187
|
|
|
188 * Fixed a rare bug about the wrong alignment coordinate when a read is
|
|
|
189 poorly aligned.
|
|
|
190
|
|
|
191 * Fixed a bug in generating the "mate-unmap" SAM tag when both ends in
|
|
|
192 a pair are unmapped.
|
|
|
193
|
|
|
194 (0.5.0: 20 August 2009, r1200)
|
|
|
195
|
|
|
196
|
|
|
197
|
|
|
198 Beta Release 0.4.9 (19 May, 2009)
|
|
|
199 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
200
|
|
|
201 Interestingly, the integer overflow bug claimed to be fixed in 0.4.7 has
|
|
|
202 not in fact. Now I have fixed the bug. Sorry for this and thank Quan
|
|
|
203 Long for pointing out the bug (again).
|
|
|
204
|
|
|
205 (0.4.9: 19 May 2009, r1075)
|
|
|
206
|
|
|
207
|
|
|
208
|
|
|
209 Beta Release 0.4.8 (18 May, 2009)
|
|
|
210 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
211
|
|
|
212 One change to "aln -R". Now by default, if there are no more than `-R'
|
|
|
213 equally best hits, bwa will search for suboptimal hits. This change
|
|
|
214 affects the ability in finding SNPs in segmental duplications.
|
|
|
215
|
|
|
216 I have not tested this option thoroughly, but this simple change is less
|
|
|
217 likely to cause new bugs. Hope I am right.
|
|
|
218
|
|
|
219 (0.4.8: 18 May 2009, r1073)
|
|
|
220
|
|
|
221
|
|
|
222
|
|
|
223 Beta Release 0.4.7 (12 May, 2009)
|
|
|
224 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
225
|
|
|
226 Notable changes:
|
|
|
227
|
|
|
228 * Output SM (single-end mapping quality) and AM (smaller mapping
|
|
|
229 quality among the two ends) tag from sam output.
|
|
|
230
|
|
|
231 * Improved the functionality of stdsw.
|
|
|
232
|
|
|
233 * Made the XN tag more accurate.
|
|
|
234
|
|
|
235 * Fixed a very rare segfault caused by integer overflow.
|
|
|
236
|
|
|
237 * Improve the insert size estimation.
|
|
|
238
|
|
|
239 * Fixed compiling errors for some Linux systems.
|
|
|
240
|
|
|
241 (0.4.7: 12 May 2009, r1066)
|
|
|
242
|
|
|
243
|
|
|
244
|
|
|
245 Beta Release 0.4.6 (9 March, 2009)
|
|
|
246 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
247
|
|
|
248 This release improves the SOLiD support. First, a script for converting
|
|
|
249 SOLiD raw data is provided. This script is adapted from solid2fastq.pl
|
|
|
250 in the MAQ package. Second, a nucleotide reference file can be directly
|
|
|
251 used with `bwa index'. Third, SOLiD paired-end support is
|
|
|
252 completed. Fourth, color-space reads will be converted to nucleotides
|
|
|
253 when SAM output is generated. Color errors are corrected in this
|
|
|
254 process. Please note that like MAQ, BWA cannot make use of the primer
|
|
|
255 base and the first color.
|
|
|
256
|
|
|
257 In addition, the calculation of mapping quality is also improved a
|
|
|
258 little bit, although end-users may barely observe the difference.
|
|
|
259
|
|
|
260 (0.4.6: 9 March 2009, r915)
|
|
|
261
|
|
|
262
|
|
|
263
|
|
|
264 Beta Release 0.4.5 (18 Feburary, 2009)
|
|
|
265 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
266
|
|
|
267 Not much happened, but I think it would be good to let the users use the
|
|
|
268 latest version.
|
|
|
269
|
|
|
270 Notable changes (Thank Bob Handsaker for catching the two bugs):
|
|
|
271
|
|
|
272 * Improved bounary check. Previous version may still give incorrect
|
|
|
273 alignment coordinates in rare cases.
|
|
|
274
|
|
|
275 * Fixed a bug in SW alignment when no residue matches. This only
|
|
|
276 affects the `sampe' command.
|
|
|
277
|
|
|
278 * Robustly estimate insert size without setting the maximum on the
|
|
|
279 command line. Since this release `sampe -a' only has an effect if
|
|
|
280 there are not enough good pairs to infer the insert size
|
|
|
281 distribution.
|
|
|
282
|
|
|
283 * Reduced false PE alignments a little bit by using the inferred insert
|
|
|
284 size distribution. This fix may be more important for long insert
|
|
|
285 size libraries.
|
|
|
286
|
|
|
287 (0.4.5: 18 Feburary 2009, r829)
|
|
|
288
|
|
|
289
|
|
|
290
|
|
|
291 Beta Release 0.4.4 (15 Feburary, 2009)
|
|
|
292 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
293
|
|
|
294 This is mainly a bug fix release. Notable changes are:
|
|
|
295
|
|
|
296 * Imposed boundary check for extracting subsequence from the
|
|
|
297 genome. Previously this causes memory problem in rare cases.
|
|
|
298
|
|
|
299 * Fixed a bug in failing to find whether an alignment overlapping with
|
|
|
300 N on the genome.
|
|
|
301
|
|
|
302 * Changed MD tag to meet the latest SAM specification.
|
|
|
303
|
|
|
304 (0.4.4: 15 Feburary 2009, r815)
|
|
|
305
|
|
|
306
|
|
|
307
|
|
|
308 Beta Release 0.4.3 (22 January, 2009)
|
|
|
309 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
310
|
|
|
311 Notable changes:
|
|
|
312
|
|
|
313 * Treat an ambiguous base N as a mismatch. Previous versions will not
|
|
|
314 map reads containing any N.
|
|
|
315
|
|
|
316 * Automatically choose the maximum allowed number of differences. This
|
|
|
317 is important when reads of different lengths are mixed together.
|
|
|
318
|
|
|
319 * Print mate coordinate if only one end is unmapped.
|
|
|
320
|
|
|
321 * Generate MD tag. This tag encodes the mismatching positions and the
|
|
|
322 reference bases at these positions. Deletions from the reference will
|
|
|
323 also be printed.
|
|
|
324
|
|
|
325 * Optionally dump multiple hits from samse, in another concise format
|
|
|
326 rather than SAM.
|
|
|
327
|
|
|
328 * Optionally disable iterative search. This is VERY SLOOOOW, though.
|
|
|
329
|
|
|
330 * Fixed a bug in generate SAM.
|
|
|
331
|
|
|
332 (0.4.3: 22 January 2009, r787)
|
|
|
333
|
|
|
334
|
|
|
335
|
|
|
336 Beta Release 0.4.2 (9 January, 2009)
|
|
|
337 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
338
|
|
|
339 Aaron Quinlan found a bug in the indexer: the bwa indexer segfaults if
|
|
|
340 there are no comment texts in the FASTA header. This is a critical
|
|
|
341 bug. Nothing else was changed.
|
|
|
342
|
|
|
343 (0.4.2: 9 January 2009, r769)
|
|
|
344
|
|
|
345
|
|
|
346
|
|
|
347 Beta Release 0.4.1 (7 January, 2009)
|
|
|
348 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
349
|
|
|
350 I am sorry for the quick updates these days. I like to set a milestone
|
|
|
351 for BWA and this release seems to be. For paired end reads, BWA also
|
|
|
352 does Smith-Waterman alignment for an unmapped read whose mate can be
|
|
|
353 mapped confidently. With this strategy BWA achieves similar accuracy to
|
|
|
354 maq. Benchmark is also updated accordingly.
|
|
|
355
|
|
|
356 (0.4.1: 7 January 2009, r760)
|
|
|
357
|
|
|
358
|
|
|
359
|
|
|
360 Beta Release 0.4.0 (6 January, 2009)
|
|
|
361 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
362
|
|
|
363 In comparison to the release two days ago, this release is mainly tuned
|
|
|
364 for performance with some tricks I learnt from Bowtie. However, as the
|
|
|
365 indexing format has also been changed, I have to increase the version
|
|
|
366 number to 0.4.0 to emphasize that *DATABASE MUST BE RE-INDEXED* with
|
|
|
367 `bwa index'.
|
|
|
368
|
|
|
369 * Improved the speed by about 20%.
|
|
|
370
|
|
|
371 * Added multi-threading to `bwa aln'.
|
|
|
372
|
|
|
373 (0.4.0: 6 January 2009, r756)
|
|
|
374
|
|
|
375
|
|
|
376
|
|
|
377 Beta Release 0.3.0 (4 January, 2009)
|
|
|
378 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
379
|
|
|
380 * Added paired-end support by separating SA calculation and alignment
|
|
|
381 output.
|
|
|
382
|
|
|
383 * Added SAM output.
|
|
|
384
|
|
|
385 * Added evaluation to the documentation.
|
|
|
386
|
|
|
387 (0.3.0: 4 January 2009, r741)
|
|
|
388
|
|
|
389
|
|
|
390
|
|
|
391 Beta Release 0.2.0 (15 Augusst, 2008)
|
|
|
392 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
393
|
|
|
394 * Take the subsequence at the 5'-end as seed. Seeding strategy greatly
|
|
|
395 improves the speed for long reads, at the cost of missing a few true
|
|
|
396 hits that contain many differences in the seed. Seeding also increase
|
|
|
397 the memory by 800MB.
|
|
|
398
|
|
|
399 * Fixed a bug which may miss some gapped alignments. Fixing the bug
|
|
|
400 also slows the speed a little.
|
|
|
401
|
|
|
402 (0.2.0: 15 August 2008, r428)
|
|
|
403
|
|
|
404
|
|
|
405
|
|
|
406 Beta Release 0.1.6 (08 Augusst, 2008)
|
|
|
407 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
408
|
|
|
409 * Give accurate CIGAR string.
|
|
|
410
|
|
|
411 * Add a simple interface to SW/NW alignment
|
|
|
412
|
|
|
413 (0.1.6: 08 August 2008, r414)
|
|
|
414
|
|
|
415
|
|
|
416
|
|
|
417 Beta Release 0.1.5 (27 July, 2008)
|
|
|
418 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
419
|
|
|
420 * Improve the speed. This version is expected to give the same results.
|
|
|
421
|
|
|
422 (0.1.5: 27 July 2008, r400)
|
|
|
423
|
|
|
424
|
|
|
425
|
|
|
426 Beta Release 0.1.4 (22 July, 2008)
|
|
|
427 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
428
|
|
|
429 * Fixed a bug which may cause missing gapped alignments.
|
|
|
430
|
|
|
431 * More clearly define what alignments can be found by BWA (See
|
|
|
432 manual). Now BWA runs a little slower because it will visit more
|
|
|
433 potential gapped alignments.
|
|
|
434
|
|
|
435 * A bit code clean up.
|
|
|
436
|
|
|
437 (0.1.4: 22 July 2008, r387)
|
|
|
438
|
|
|
439
|
|
|
440
|
|
|
441 Beta Release 0.1.3 (21 July, 2008)
|
|
|
442 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
443
|
|
|
444 Improve the speed with some tricks on retrieving occurences. The results
|
|
|
445 should be exactly the same as that of 0.1.2.
|
|
|
446
|
|
|
447 (0.1.3: 21 July 2008, r382)
|
|
|
448
|
|
|
449
|
|
|
450
|
|
|
451 Beta Release 0.1.2 (17 July, 2008)
|
|
|
452 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
453
|
|
|
454 Support gapped alignment. Codes for ungapped alignment has been removed.
|
|
|
455
|
|
|
456 (0.1.2: 17 July 2008, r371)
|
|
|
457
|
|
|
458
|
|
|
459
|
|
|
460 Beta Release 0.1.1 (03 June, 2008)
|
|
|
461 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
462
|
|
|
463 This is the first release of BWA, Burrows-Wheeler Alignment tool. Please
|
|
|
464 read man page for more information about this software.
|
|
|
465
|
|
|
466 (0.1.1: 03 June 2008, r349)
|
|
|
467
|
|
|
468
|
|
|
469
|
