Bowtie 2

Fast and sensitive read alignment
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. Open Source Software

Site Map

Latest Release

Bowtie2 2.1.0 2/21/13 

Please cite: Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012, 9:357-359.

Related Tools

Bowtie: Ultrafast short read alignment
Crossbow: Genotyping, cloud computing
Myrna: Cloud, differential gene expression
Tophat: RNA-Seq splice junction mapper
Cufflinks: Isoform assembly, quantitation

Indexes

H. sapiens, UCSC hg18 3.5 GB
 or: part 1 (1.5 GB), part 2 (651 MB), part 3 (1.5 GB)
H. sapiens, UCSC hg19 3.5 GB
 or: part 1 (1.5 GB), part 2 (650 MB), part 3 (1.5 GB)
M. musculus, UCSC mm10 3.2 GB
 or: part 1 (1.3 GB), part 2 (600 MB), part 3 (1.3 GB)
M. musculus, UCSC mm9 3.2 GB
 or: part 1 (1.3 GB), part 2 (593 MB), part 3 (1.3 GB)
R. norvegicus, UCSC rn4 3.1 GB
 or: part 1 (1.3 GB), part 2 (580 MB), part 3 (1.3 GB)

Some unzip programs cannot handle archives >2 GB. If you have problems downloading or unzipping a >2 GB index, try downloading in parts.

Related publications

Author

Other Documentation

  • Bio. of Genomes poster, 5/11 (.ppt, .pdf)

Links

Version 2.1.0 - February 21, 2013

  • Improved multithreading support so that Bowtie 2 now uses native Windows threads when compiled on Windows and uses a faster mutex. Threading performance should improve on all platforms.
  • Improved support for building 64-bit binaries for Windows x64 platforms.
  • Bowtie 2 uses a lightweight mutex by default.
  • Test option --nospin is no longer available. However bowtie2 can always be recompiled with EXTRA_FLAGS="-DNO_SPINLOCK" in order to drop the default spinlock usage.

Version 2.0.6 - January 27, 2013

  • Fixed issue whereby spurious output would be written in --no-unal mode.
  • Fixed issue whereby multiple input files combined with --reorder would cause truncated output and a memory spike.
  • Fixed spinlock datatype for Win64 API (LLP64 data model) which made it crash when compiled under Windows 7 x64.
  • Fixed bowtie2 wrapper to handle filename/paths operations in a more platform independent manner.
  • Added pthread as a default library option under cygwin, and pthreadGC for MinGW.
  • Fixed some minor issues that made MinGW compilation fail.

Version 2.0.5 - January 4, 2013

  • Fixed an issue that would cause excessive memory allocation when aligning to very repetitive genomes.
  • Fixed an issue that would cause a pseudo-randomness-related assert to be thrown in debug mode under rare circumstances.
  • When bowtie2-build fails, it will now delete index files created so far so that invalid index files don't linger.
  • Tokenizer no longer has limit of 10,000 tokens, which was a problem for users trying to index a very large number of FASTA files.
  • Updated manual's discussion of the -I and -X options to mention that setting them farther apart makes Bowtie 2 slower.
  • Renamed COPYING to LICENSE and created a README to be GitHub-friendly.

Version 2.0.4 - December 17, 2012

  • Fixed issue whereby --un, --al, --un-conc, and --al-conc options would incorrectly suppress SAM output.
  • Fixed minor command-line parsing issue in wrapper script.
  • Fixed issue on Windows where wrapper script would fail to find bowtie2-align.exe binary.
  • Updated some of the index-building scripts and documentation.
  • Updated author's contact info in usage message

Version 2.0.3 - December 14, 2012

  • Fixed thread safely issues that could cause crashes with a large number of threads. Thanks to John O’Neill for identifying these issues.
  • Fixed some problems with pseudo-random number generation that could cause unequal distribution of alignments across equally good candidate loci.
  • The --un, --al, --un-conc, and --al-conc options (and their compressed analogs) are all much faster now, making it less likely that they become the bottleneck when Bowtie 2 is run with large -p.
  • Fixed issue with innaccurate mapping qualities, XS:i, and YS:i flags when --no-mixed and --no-discordant are specified at the same time.
  • Fixed some compiler warnings and errors when using clang++ to compile.
  • Fixed race condition in bowtie2 script when named pipes are used.
  • Added more discussion of whitespace in read names to manual.

Sourceforge spam

  • Spam on the sourceforge tracker (i.e. where feature requests and bug reports go) was getting out of control, so I disabled posting by anonymous users. This means you'll have to use some set of credentials when posting on the tracker. Sourceforge allows you to use various, e.g., your Google credentials. Sorry for the invonvenience, but I think this will make the experience better overall.

Version 2.0.2 - October 31, 2012

  • Fixes a couple small issues pointed out to me immediately after 2.0.1 release
  • Mac binaries now built on 10.6 in order to be forward-compatible with more Mac OS versions
  • Small changes to source to make it compile with gcc versions up to 4.7 without warnings

Version 2.0.1 - October 31, 2012

  • First non-beta release.
  • Fixed an issue that would cause Bowtie 2 to use excessive amounts of memory for closely-matching and highly repetitive reads under some circumstances.
  • Fixed a bug in --mm mode that would fail to report when an index file could not be memory-mapped.
  • Added --non-deterministic option, which better matches how some users expect the pseudo-random generator inside Bowtie 2 to work. Normally, if you give the same read (same name, sequence and qualities) and --seed, you get the same answer. --non-deterministic breaks that guarantee. This can be more appropriate for datasets where the input contains many identical reads (same name, same sequence, same qualities).
  • Fixed a bug in bowtie2-build would yield corrupt index files when memory settings were adjusted in the middle of indexing.
  • Clarified in manual that --un-* options print reads exactly as they appeared in the input, and that they are not necessarily written in the same order as they appeared in the input.
  • Fixed issue whereby wrapper would incorrectly interpret arguments with --al as a prefix (e.g. --all) as --al.