1 Bowtie: an Ultrafast, Lightweight Short Read Aligner
6 Bowtie is now available for download. 0.9.0 is the first version to
7 be released under the OSI Artistic License (see `COPYING') and freely
8 available to the public for download. The current version is 0.12.7.
13 Please report any issues using the Sourceforge bug tracker:
15 https://sourceforge.net/tracker/?group_id=236897&atid=1101606
20 To receive announcements (including release announcements) about Bowtie
21 and related tools (including Crossbow, TopHat, Cufflinks, Myrna)
22 subscribe to our mailing list:
24 https://lists.sourceforge.net/lists/listinfo/bowtie-bio-announce
26 Version Release History
27 =======================
29 Version 0.12.7 - September 7, 2010
30 * Fixes the all-gap reference sequence issue that was present in
31 Bowtie 0.12.6. Index files produced by bowtie-build 0.12.5 and
32 earlier (back to 0.10.*) are compatible with bowtie 0.12.7. Index
33 files produced by bowtie-build 0.12.7 are backward compatible with
34 bowtie 0.12.5 and earlier as long as the first reference sequence
35 is not all-gaps (or, when colorspace indexes, as long as the first
36 reference sequence has two consecutive ACGT characters in it
38 * Indexes where the first sequence consists of all gaps or other
39 non-ACGT characters are not handled properly by Bowtie versions
40 0.12.5 and older, but are handled properly by Bowtie 0.12.7.
41 * REMOVED: bowtie-build's --old-reverse option; the old reverse-
42 index scheme is again the default. The new scheme is disabled
43 pending further refinement.
46 * The version of bowtie-build distributed in Bowtie 0.12.6 IS
47 BROKEN. It could not handle stretches of ambiguous reference
48 characters compatibly with prior versions of Bowtie. Please use
49 Bowtie 0.12.5's bowtie-build instead. Bowtie 0.12.7, due out
50 soon, will contain a complete set of working tools. Bowtie 0.12.7
51 will revert to old way of building the reverse index. Sorry for
54 Version 0.12.6 - August 29, 2010
55 * Modified bowtie-inspect's default mode to use the bit-encoded
56 reference portion of the index to reconstruct the reference
57 sequence, rather than the ebwt portion. This makes bowtie-inspect
58 much faster and uses less memory, and the output for a colorspace
59 index will now be in nucleotide space. To get the behavior of the
60 old default, use the new -e/--ebwt-ref option.
61 * Fixed bug whereby SOLiD QV strings would fail to parse.
62 * Moved to a new default way of building the reverse index. Revert
63 to the old behavior with bowtie-build's new --old-reverse option.
64 The new reverse index format is forward and backward compatible
65 with `bowtie`, unless otherwise noted in a future version.
66 * Fixed issue that would sometimes cause bowtie-build to crash when
67 building a large index with a low --offrate.
68 * Fixed build issue that would cause bowtie-build built on one
69 version of Linux to die with a "floating point error" on other
71 * Fixed a bug whereby alignment cost could sometimes be
72 miscalculated. Stratum was unaffected.
73 * bowtie now simply skips reads with 0 characters. Previously it
74 would print an error and exit.
76 Version 0.12.5 - April 10, 2010
77 * Fixed spurious "Error while writing string output; not all
78 characters written" errors in -S/--sam mode.
80 Version 0.12.4 - April 5, 2010
81 * Periods in read sequences are now treated as Ns instead of
82 ignored. This should help with some problems where Bowtie
83 erroneously reports "Reads file contained a pattern with more than
84 1024 quality values..." for data from recent versions of the
86 * Fixed a bug whereby some error and warning messages would be
87 printed on top of each other in -p mode.
88 * Chunk-exhaustion warnings messages are now suppressed when --quiet
90 * Fixed small issue in quality decoding whereby no-confidence colors
91 would incorrectly influence decoded quality of adjacent bases.
93 Version 0.12.3 - February 17, 2010
94 * Fixed a significant bug in -C/--color mode whereby quality values
95 for SNP nucleotide positions were erroneously penalized.
96 * Fixed a bug in -S/--sam mode whereby if whitespace occurred in the
97 original read name, it would be printed in the QNAME field in
98 violation of the SAM spec. Bowtie now truncates read names at the
99 first whitespace character before printing.
100 * When input is FASTQ and -C/--color is enabled, Bowtie is now
101 tolerant of output from FASTQ converters that include the primer
102 base and where the quality string is one character shorter than
103 the sequence string (due to the primer). This fixes issues users
104 have reported using output from BFAST's solid2fastq.
105 * Added support for SOLiD-style _QV files, via the -Q/--quals, --Q1
106 and --Q2 options. These options are used in combination with
107 -C/--color and -f to align parallel colorspace read/quality files
108 without having to convert to FASTQ.
110 Version 0.12.2 - February 2, 2010
111 * When -C/--color is enabled, the default paired-end orientation is
112 now --ff, not --fr. The new default fits typical SOLiD output.
113 * Fixed a bug whereby very large reads could cause bowtie to crash
115 * After 0.12.1, some issues remained whereby bowtie would fail to
116 trim the primer in colorspace (e.g. in -c mode). All input modes
117 should now have fully-functioning
118 * Fixed a bug whereby decoded colorspace qualities could overflow
119 and erroneously become low qualities.
120 * Fixed a bug that could produce incorrect paired-end alignment
121 results in -n mode when using paired-end orientation modes other
122 than --fr. Even with the bug, reported results are reasonable;
123 but the seed edit constraint (-n) may have been applied to the
124 wrong end of one of the mates.
125 * Changed --chunkmbs default up to 64 from 32.
126 * Better error checking and reporting for some bowtie options.
127 * Some basic testing scripts are now bundled with Bowtie (in
128 scripts/test), which should make it easier to regression-test.
130 Version 0.12.1 - January 8, 2010
131 * IMPORTANT: Fixed bug whereby bowtie would fail to remove both the
132 primer base and the first color when parsing .csfasta files with
133 primer bases in -C -f mode. A workaround for users of version
134 0.12.0 is to use "-5 1" in that situation.
135 * Fixed bug whereby, when -M limit was exceeded for an unpaired
136 read, the number printed in the 7th column for the random
137 alignment was too low by 1.
138 * Added documentation discussing a pitfall regarding SOLiD paired-
139 end input, i.e., not all entries necessarily have corresponding
140 mates in the other file.
142 Version 0.12.0 - December 23, 2009
143 * Added missing README.markdown file
144 * Minor documentation additions
146 Version 0.12.0-beta1 - December 12, 2009
147 * Added SOLiD colorspace support
148 * Colorspace indexes are distinct from standard letterspace
149 indexes and must be built with a separate invocation of
150 bowtie-build (with -C option)
151 * Running bowtie with -C causes Bowtie to align in colorspace;
152 both index and reads must be in colorspace
153 * Colorspace memory requirement is the same as paired-end
154 alignment in nucleotide-space (normal) mode. Paired-end
155 alignment does not increase the memory requirement further in
157 * csfasta, csfastq, and "raw" read formats are all supported with
158 -C; '0' means "blue" and is intechangeable with 'A', likewise
159 '1' ('C') means "green", '2' ('G') means "orange" and '3' ('T')
161 * Colorspace versions of pre-built indexes added (see Bowtie web
163 * New manual section discussing colorspace features
164 * Fixed a few SAM output issues
165 * @PG line now properly uses colons instead of equals signs
166 * Removed /1, /2 suffixes for paired-end reads in SAM mode
167 * Added --sam-RG option that permits the user to insert set values
168 for flags that appear on the @RG line
169 * Fixed lingering pthreads bugs that would cause Bowtie to hang or
170 crash toward the end of execution with -p > 1.
171 * Fixed performance-related bug that would cause paired-end
172 alignment to be artificially slow in many situations.
173 * Fixed issue with random number generation that would result in
174 non-random selection of alignments in some situations.
175 * bowtie -f now supports fasta files with reads split across
177 * New --suppress option suppresses unwanted columns of output
178 * The MANUAL file was converted to markdown format, facilitating
179 conversion to various other formats using tools like pandoc
180 * DEPRECATED: bowtie: --concise, bowtie-build: --big, --little
181 * REMOVED: -z/--phased, -b/--binout, bowtie-maptool,
184 Version 0.11.3 - October 12, 2009
185 * Fixed crashing bug in -S/--sam mode when the number of reference
186 sequences in the index is very large.
187 * Added --sam-nohead option to suppress output of SAM headers in
189 * Added --sam-nosq option to suppress output of @SQ SAM headers in
190 -S/--sam mode. These can become a nuisance when the reference
191 index contains a very large number of sequences.
192 * Fixed a bug in bowtie-build's auto-configure mode that would cause
193 it to underestimate the amount of memory required by a set of
194 parameters. This in turn would cause the index to be corrupted.
196 Version 0.11.2 - October 7, 2009
197 * Fixed issue whereby --max option was disabled.
199 Version 0.11.1 - October 5, 2009
200 * SAM output: changed XS:i optional field to be named XA:i to avoid
201 a conflict with TopHat's XS:i field.
203 Version 0.11.0 - October 5, 2009
204 * Initial SAM output support with -S/--sam option. Bowtie sets all
205 fields according to the SAM spec (Version 0.1.2-draft, 20090820).
206 See the new "SAM Output" section of the manual for details.
207 * Added --shmem option: --shmem is similar to --mm in that it allows
208 concurrent 'bowtie' processes querying the same index to share a
209 single memory image of the index. Unlike --mm, shared memory
210 alocated by --shmem is permanent.
211 * The alignment summary printed to stderr at the end of an alignment
212 run is now more friendly and includes data about the number and
213 proportion of reads that aligned, failed to align, or were
214 suppressed via the -m option.
215 * When too-short reads are encountered, Bowtie now always prints
216 warnings, not errors. --quiet now suppresses those warnings.
217 * By default, when bowtie prints a reference sequence name it now
218 stops at the first whitespace. In 0.10.1, the default was to
219 print the entire name, which could cause confusion when parsing
220 Bowtie output. To revert to printing the full name, use the new
222 * Bowtie now prints the command-line before exiting with an error.
223 * Fixed mistake in the manual's "Default output" section: the offset
224 in field 4 is 0-based, not 1-based. To obtain a 1-based offset
225 instead, use the -B 1 option.
226 * Various minor bug fixes.
227 * DEPRECATED: -z/--phased, -b/--binout, bowtie-maptool,
228 bowtie-maqconvert. These features will be removed in a future
229 version of Bowtie. Note that -b/--binout, bowtie-maptool, and
230 bowtie-maqconvert are largely superseded by the SAM output format
231 (-S/--sam), BAM, and SAMtools (http://samtools.sf.net). Contact
232 the authors if this is a problem.
233 * REMOVED: --unfq/--unfa/--maxfq/--maxfa/--alfq/--alfa. Please use
234 --un/--max/--al instead. Contact the authors if this is a
237 Version 0.10.1 - July 19, 2009
238 * Now when -3/-5 are used in combination with -I/-X, the -I/-X
239 constraints are interpreted as applying to the original insert,
240 not the trimmed insert.
241 * Fixed issue whereby -I option was ignored; -I option works now.
242 * Fixed a bug whereby some large indexes were incorrectly reported
243 as corrupt by bowtie-build.
244 * Fixed issue whereby negative quality values were wrongly rejected
245 when both --integer-quals and --solexa-quals were specified.
246 * The -l/--seedlen parameter can now be adjusted down to 5
247 (previously had to be >= 20).
248 * Fixed several minor memory leaks and out-of-bounds issues. The
249 Linux version of the bowtie aligner now receives a clean bill of
250 health from valgrind's memcheck.
251 * Other minor bugfixes.
253 Version 0.10.0.2 - 6/28/09
254 * Second bugfix for Windows version. src and bin-win32 packages
255 updated. Linux and Mac users are not affected. Thanks for your
256 bug reports and patience.
258 Version 0.10.0.1 - 6/23/09
259 * Fix for crashing bug in Windows version. src and bin-win32
260 packages updated. Linux and Mac users are not affected.
262 Version 0.10.0 - June 12, 2009
263 * Major change: All alignment modes are now unstratified by default.
264 The --nostrata option has been removed, since it is now the
265 default. A --strata option has been added to override the default
266 and force stratified reporting. Reporting is stratified if and
267 only if --strata is specified. --strata now cannot be specified
268 without also specifying --best. Please note that, because of this
269 change, specifying the same arguments to this version of Bowtie
270 may yield different reported results.
271 * Replaced the --unfa/--unfq options with a single --un option,
272 which writes unaligned reads to an output file (or pair of output
273 files) but keeps reads in their original form. This is in
274 contrast to the old --unfa/--unfq options, which only supported
275 FASTA or FASTQ formats, and which would print a post-trimming and
276 post-quality-value translation version of the read. Likewise, the
277 --alfa/--alfq and --maxfa/--maxfq options have been replaced with
278 --al and --max options. The old options are still present, but
279 are deprecated and will be removed in a future version.
280 * Added --nofw and --norc options, allowing alignment to just one
281 reference strand or the other.
282 * Added --mm option that causes bowtie to use memory-mapped files
283 instead of traditional file I/O to access the reference index.
284 This allows multiple bowtie processes running on the same computer
285 to share a single in-memory image of a given index. This is a
286 useful feature for parallelizing bowtie in situations where memory
287 is limited and where -p is inappropriate or insufficient. This
288 feature is not available in the Windows version of Bowtie.
289 * Added a section to the manual ("Reporting Modes") clarifying and
290 giving examples of how to use Bowtie's reporting options.
291 * The --al and -z/--phased options previously interacted in such a
292 way that the --al file could contain multiple entries for the same
293 aligned read. --al and -z/--phased are now incompatible.
294 * The --oldpmap option, deprecated in version 0.9.8, has been
297 Version 0.9.9.3 - May 12, 2009
298 * Fixed an issue where bowtie --best would sometimes use excessive
299 amounts of memory to store path descriptors. There is now a per-
300 thread 32-MB ceiling (configurable with new option --chunkmbs
301 <int>) on the memory taken by path descriptors. If the ceiling is
302 exceeded Bowtie will skip the offending read, print a warning
303 message identifying the read, and continue.
304 * More options are available for defining the quality-value format,
305 including new --phred64-quals/--solexa1.3-quals options
306 appropriate for the 64-based-Phred output of Illumina's GA
307 Pipeline 1.3. Added option --phred33-quals to to handle the more
308 typical 33-based-Phred scale (the default). The --solexa-quals
309 option still handles the 64-based-Solexa scale output by GA
310 Pipeline versions prior to 1.3.
311 * bowtie-build now checks output files for obvious corruption due,
312 for example, to disk exhaustion.
313 * Specifying "-" (meaning stdin) as an input to bowtie is now
314 supported and documented.
315 * Fixed a bug whereby bowtie-maqconvert could fail to notice that it
316 had exhausted memory and output a corrupt Maq map file.
317 * Fixed a bug whereby bowtie would crash when trying to use an index
318 built on a machine with different endianness.
319 * Fixed several issues that prevented Bowtie from compiling on
320 Solaris. I confirm that Bowtie builds and runs on Solaris.
321 * Added _LARGEFILE_SOURCE _FILE_OFFSET_BITS=64 _GNU_SOURCE to the
322 default build options in an attempt to resolve some of the large-
323 file issues users are having.
324 * Clarified column 7 in the manual. We received many queries from
325 users curious about this number.
326 * Moderate speed improvements in --best mode.
328 Version 0.9.9.2 - April 6, 2009
329 * Paired-end alignment is now available in all alignment modes,
330 including all -n modes.
331 * --best now provides better guarantees. Reported alignments are
332 now guaranteed to be "best" both in terms of stratum (i.e. number
333 of mismatches, or mismatches in the seed in the case of -n mode),
334 and in terms of the quality values at the mismatched position(s).
335 Stratum always trumps quality when determining best alignments.
336 Also, --best mode resolves the strand bias issue (see manual for a
337 discussion of the issue).
338 * Speed improvements for --best mode in most alignment modes.
339 * Major speed improvement for the -v 3 alignment mode (except when
341 * The "Reported X alignments..." message is now printed to stderr
342 rather than stdout. Only alignments are written to stdout.
343 * In bowtie-maqconvert, read names longer than Maq's limit (36) are
344 now truncated to a suffix of the original name, rather than a
345 prefix. This mimics Maq's behavior and prevents "/1" and "/2"
346 suffixes for paired-end reads from being destroyed.
347 * Added --alfq/--alfa options to dump aligned reads to FASTQ and/or
349 * Removed many extraneous source files.
351 Version 0.9.9.1 - March 10, 2009
352 * Added paired-end alignment for -v 2 and -v 3 alignment modes (-n
354 * Minor bug fixes and speed improvements for all paired-end modes.
355 * Added -s/--skip <int> option to skip over the first <int> reads or
357 * --unfq/--unfa/--maxfq/--maxfa modes no longer create empty output
359 * All Bowtie tools now compile under GCC 4.3.3.
360 * Fixed bug whereby bowtie -b would sometimes write garbage into the
361 reference offset field.
362 * Paired-end info is now persisted in the -b format, allowing
363 bowtie-maptool output to add "/1" and "/2" suffixes as
366 Version 0.9.9 - February 19, 2009
367 * Added some preliminary support for paired-end alignment in -v 0
368 and -v 1 modes. -1/-2 options to specify the paired-end files,
369 -I/-X to specify min and max insert sizes, and --fr/--rf/--ff
370 specify relative orientation of upstream and downstream mates.
371 bowtie-build now builds two additional files: NAME.3.ebwt and
372 NAME.4.ebwt. Together, these files store a bitpacked version of
373 the reference and they are required for paired-end alignment. If
374 your index does not include these files and you would like to
375 perform a paired-end alignment, you will have to rebuild the index
376 with bowtie-build version 0.9.9 or later. Paired-end alignment is
377 not compatible with -z mode, and it incurs about a 30% greater
378 memory overhead than single-end mode.
379 * Pre-built indexes available from Bowtie website have been updated
380 to include .3/.4.ebwt index files. These new pre-built indexes
381 are no longer compatible with bowtie versions prior to 0.9.8.
382 * New -B/--offbase option allows user to specify how bowtie numbers
383 reference positions in its output. E.g. -B 1 causes bowtie to
384 number leftmost char as 1. -B 0 is the default, but -B 1 will
385 likely become the default in the 1.0 release.
386 * Fixed a bug that caused trimming options -3 and -5 not to work
387 properly in -r (raw input) mode.
388 * bowtie-build now prints a friendly error message and exits if an
389 input file doesn't exist.
390 * Fixed a bug that caused the Win32 version of bowtie to hang just
391 before it would normally have exited.
392 * Fixed bug that could prevent successful read-in of very large
393 (>1GB) .2.ebwt index files.
394 * Removed --maxns option since it's mostly redundant with what -v
396 * Removed --ntoa option.
397 * bowtie usage message is now divided into sections for clarity.
399 Version 0.9.8.1 - January 7, 2009
400 * Fixed all known problems with the --unfa/--unfq options:
401 * They now work properly with multiple threads.
402 * Fixed issue where sequence and quals were sometimes reversed.
403 * Fixed other issues causing spurious omission of unaligned reads.
404 * Added --maxfa/--maxfq options so that reads that don't align due
405 to the -m limit can be dumped separately from reads that don't
407 * Alignment output is now guaranteed to be "deterministic" even when
408 multiple threads are used. I.e., given the same input reads (in
409 any order) and the same --seed, bowtie will produce the same
410 alignments every time it is run, though not necessarily in the
411 same order. This does not hold across different versions of
413 * Multiple other bug fixes.
415 Version 0.9.8 - November 25, 2008
416 * --unfa/--unfq <filename> options cause bowtie to dump unaligned
417 reads to FASTA and/or FASTQ files.
418 * bowtie-build now selects its memory-efficiency parameters (--bmax,
419 --dcv, --packed) automatically by default; this makes it far
420 easier to build an index under memory constraints by eliminating
421 tedious trail-and-error. New -a option disables this, yielding
423 * bowtie-build-packed is no longer a separate binary. Supplying the
424 new -p/--packed argument to bowtie-build is the new equivalent.
425 * New tool bowtie-maptool converts between Bowtie's output formats.
426 * New tool bowtie-inspect recreates reference strings from Bowtie
428 * Renamed bowtie-convert to bowtie-maqconvert for clarity.
429 * New universal Mac binary combines i386 & x86_64 binaries. PowerPC
431 * Added --nomaqround option to bowtie.
432 * Fixed memory leaks in bowtie.
433 * Switched to a new scheme for mapping positions in "joined"
434 reference string to positions in original strings. This changes
435 the index format. bowtie-build's --oldpmap parameter reverts to
436 the old format. Versions of bowtie prior to 0.9.8 cannot search
437 indexes produced by bowtie-build 0.9.8 unless bowtie-build is run
438 with --oldpmap. bowtie 0.9.8 can search either index format.
439 Pre-built indexes are still in the old format, but will switch to
440 new format when Bowtie 1.0 is released.
442 Version 0.9.7.1 - November 11, 2008
443 * Fixed an issue that caused a spurious loss of sensitivity between
444 Bowtie versions 0.9.6 and 0.9.7 in certain modes. Many thanks to
445 Ali Mortazavi for bringing this to our attention.
447 Version 0.9.7 - November 8, 2008
448 * Added new reporting option -m <int> which suppresses all
449 alignments for a particular read if more than <int> reportable
450 alignments exist for it.
451 * Threads now buffer all alignments for a particular read/phase then
452 output all alignments in one critical section. This guarantees
453 that all alignments for a given read/phase appear in one
454 consecutive block of the output, even when multiple threads are
455 operating in parallel.
456 * Separated the quality-conversion and parsing aspects of the old
457 --solexa-quals argument into separate arguments: --solexa-quals
458 (quality conversion) and --integer-quals (parsing).
459 * bowtie-convert now handles the new (post-0.7.0) Maq alignment
460 format. The new format allows Maq tools to handle reads up to
461 127 bases, whereas the old format was limited to 63 bases. Added
462 a -o option to opt for the old Maq format.
463 * New --refout argument sends alignments to a set of files named
464 refXXXXX.map, where XXXXX is the 0-padded index of the reference
465 sequence aligned to. Useful for dealing with large datasets
466 aligned to, e.g., the assembled human genome.
467 * Improved tutorial to use a simple simulated read set (included)
468 to do SNP calls with Maq.
469 * Added --nota option to bowtie-build
470 * Fixed make_h_sapiens_asm.sh script to include mitochondrial DNA.
472 Version 0.9.6 - October 10, 2008
473 * 'bowtie' now supports a host of options that allow the user to
474 specify which and how many valid alignments to report per read.
475 The default is still to report 1 "good" alignment, which is by far
476 the fastest mode. See -k/-a/--best/--nostrata options described
477 in the manual for details.
478 * 'bowtie' now supports reads up to 1024 bases long. Note that for
479 reads much longer than, say, 35 bases, the user must be careful to
480 set alignment policy parameters (especially -e) appropriately.
481 * --fast flag eliminated, double-index mode is now the default.
482 Added the -z/--phased flag to revert to phased, half-index mode.
483 * --concise output mode now officially supported. Now outputs one
485 * Changed 'bowtie-build' default back to --bmaxdivn 4.
486 * -h/--help now prints much more verbose help for 'bowtie' and
487 'bowtie-build' (verbatim from MANUAL file)
488 * BWT-searching code streamlined; much old code eliminated
490 Version 0.9.5 - September 27, 2008
491 * Last column of output now additionally reports the reference and
492 query bases (in that order) for mismatches. E.g., old: "30,32",
493 new: "30:C>A,32:C>T".
494 * Eliminated spurious trailing space in first column of output.
495 * Minor performance and sensitivity improvements.
496 * New option '-p' spawns a user-specified number of pthreads for
497 parallel processing of reads. For example, use '-p 4' to run
498 'bowtie' on 4 processor cores simultaneously.
499 * Due to the new '-p' option, 'bowtie' needs pthreads to compile and
500 run. To compile 'bowtie' without pthreads support (which disables
501 the '-p' option), use 'make BOWTIE_PTHREADS=0'.
502 * Also due to '-p' option, the Windows version of Bowtie now comes
503 with the pthreadGC2.dll file from the pthreads for Win32 project
504 (http://sourceware.org/pthreads-win32). This library is released
505 under the LGPL license.
506 * New option '--fast' causes Bowtie to load both the "forward" and
507 "mirror" halves of the index at once, which eliminates the need
508 for multiple phases and speeds up matching at the cost of using
509 about twice as much memory. '--fast' also causes 'bowtie' to
510 scale better when used in combination with '-p'.
511 * Fixed crashing bug with -o/--offrate in 'bowtie'.
512 * Improved error reporting.
514 Version 0.9.4 - September 16, 2008
515 * New method for handling gaps and ambiguity codes in the reference.
516 New 'bowtie-build' method handles long stretches of gaps
517 gracefully. New 'bowtie' rejects alignments that overlap a gap or
518 ambiguous character in the reference.
519 * Due to above change, index file format has been changed. All
520 pre-built indexes available on this site have been updated to the
521 new format. To obtain indexes with the old format, contact us.
522 * In 'bowtie' unnamed reads are now given ordinal names (rather than
523 "default") in the alignment output. Works for all input modes.
524 * New 'bowtie' input mode: Raw, activated with -r. Expects one read
525 sequence per line; no quality values or names.
526 * Fixed 'bowtie' bug whereby trimming did not work in -c mode.
527 * Changed 'bowtie-build' default to not use blockwise mode.
528 * Changed 'bowtie-build' to avoid certain infinite-loop and very-
529 long-runtime scenarios.
530 * Packaging improvements: archives now explode into subdirectories
531 and scripts are executable.
533 Version 0.9.3 - September 6, 2008
534 * Major reference-name bug fixes to bowtie-convert
536 Version 0.9.2 - September 4, 2008
537 * Now allows 3-mismatches: -n and -v options accept 3
538 * Output format prints reference name instead of id in third column
539 * Pre-built indexes updated to encode reference names
540 * Ns in reads now match nothing (previously, they matched As/Ts)
541 * Dropped -l/--linerate and -i/--linesperside arguments to bowtie-
543 * Fixed bug in Maq-like mode that allowed some poor alignments
544 * Minor speed improvements
546 Version 0.9.1 - August 25, 2008
547 * Integrated relevant SeqAn-1.1 sources into Bowtie source release
548 * Now builds on Windows under MinGW (needs pthreads and zlib)
549 * Binary releases for Linux (i386, x86_64), Windows (i386) and MacOS
552 Version 0.9.0 - August 18, 2008
553 * First stable release of Bowtie.
554 * Includes the three core Bowtie tools: the indexer 'bowtie-build',
555 the read aligner 'bowtie' and the converter from Bowtie's to Maq's
556 mapping output format, 'bowtie-convert'.
557 * Compatible pre-built indexes for many model organisms are
558 available from http://bowtie-bio.sf.net.
559 * FASTA, FASTQ inputs supported; tested with Solexa FASTQ
560 * Supports Maq alignment policy (-n and -e behave as in Maq)
561 * Supports X-mismatch policy (-v option behaves as in SOAP)
562 * -n and -v options accept 0, 1, or 2
projects / bowtie.git / blob