An ultrafast memory-efficient short read aligner

Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end). Open Source Software

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Pre-built indexes

Consider using Illumina's iGenomes collection. Each iGenomes archive contains pre-built Bowtie and Bowtie 2 indexes.

H. sapiens, UCSC hg18 2.7 GB
 or: part 1 - 1.7 GB, part 2 - 1.0 GB
 colorspace: full, or part 1, part 2
H. sapiens, UCSC hg19 2.7 GB
 or: part 1 - 1.7 GB, part 2 - 1.0 GB
 colorspace: full, or part 1, part 2
H. sapiens, NCBI v36 2.7 GB
 or: part 1 - 1.7 GB, part 2 - 1.0 GB
 colorspace: full, or part 1, part 2
H. sapiens, NCBI v37 2.7 GB
 or: part 1 - 1.7 GB, part 2 - 1.0 GB
 colorspace: full, or part 1, part 2
M. musculus, UCSC mm8 2.4 GB
 or: part 1 - 1.5 GB, part 2 - 900 MB
 colorspace: full, or part 1, part 2
M. musculus, UCSC mm9 2.4 GB
 or: part 1 - 1.5 GB, part 2 - 900 MB
 colorspace: full, or part 1, part 2
M. musculus, NCBI v37 2.4 GB
 or: part 1 - 1.5 GB, part 2 - 900 MB
 colorspace: full, or part 1, part 2
R. norvegicus, UCSC rn4 2.4 GB
 or: part 1 - 1.5 GB, part 2 - 900 MB
 colorspace: full, or part 1, part 2
B. taurus, UMD v3.0 2.4 GB
 or: part 1 - 1.5 GB, part 2 - 900 MB
 colorspace: full, or part 1, part 2
C. familiaris, UCSC canFam2 2.4 GB
 or: part 1 - 1.5 GB, part 2 - 900 MB
 colorspace: full, or part 1, part 2
G. gallus, UCSC, galGal3 1.1 GB
 colorspace: full
D. melanogaster, Flybase, r5.22 150 MB
 colorspace: full
A. thaliana, TAIR, TAIR9 120 MB
 colorspace: full
C. elegans, Wormbase, WS200 75 MB
 colorspace: full
S. cerevisiae, CYGD 15 MB
 colorspace: full
E. coli, NCBI, st. 536 5 MB
 colorspace: full

All indexes are for assemblies, not contigs. Unplaced or unlocalized sequences and alternate haplotype assemblies are excluded.

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

Check .zip file integrity with MD5s.


Other Documentation



Recent news

1.1.1 - 10/1/2014

  • Fixed a compiling linkage problem related with Mavericks OSX.
  • Improved performance for cases where the reference contains ambiguous or masked nucleobases represented by Ns.
  • Some minor automatic tests updates.

1.1.0 - 7/19/2014

  • Added support for large and small indexes, removing 4-billion-nucleotide barrier. Bowtie can now be used with reference genomes of any size.
  • No longer releasing 32-bit binaries. Simplified manual and Makefile accordingly.
  • Phased out CygWin support.
  • Improved efficiency of index files loading.
  • Fixed a bug that made bowtie-inspect fail in some situations.
  • (This release was briefly given version number 2.0.0, but we changed it to 1.1.0 to avoid confusion with Bowtie 2.)

1.0.1 release - 3/14/2014

  • Improved index querying efficiency using "population count" instructions available since SSE4.2.
  • Credits to the Intel(r) enabling team for performance optimizations included in this release. Thank you!

Bowtie on GitHub - 4/11/13

1.0.0 release - 4/9/13

  • Finally, a 64-bit Windows binary!
  • Due to general performance improvements spinlocking is now used by default. The EXTRA_FLAGS=-DNO_SPINLOCK may be used to reverse this during compilation.
  • Fixed some race conditions.
  • CygWin builds now use pthreads library.
  • Changed MinGW to optionally use pthread library on Win32 platforms.
  • Changed the Windows build to use native Windows threads by default.
  • Renamed COPYING to LICENSE to be more GitHub-friendly.
  • 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.
  • Removed references to no-longer-implemented --cutoff option for bowtie-build

0.12.9 release - 12/16/12

  • Fixed a bug whereby read names would not be truncated at first whitespace character in unmapped or maxed-out SAM records.
  • Fixed errors and warnings when compiling with clang++.
  • Fixed most errors and warnings when compiling with recent versions of g++, though you may need to add EXTRA_FLAGS=-Wno-enum-compare to avoid all warnings.

0.12.8 release - 5/6/12

  • Fixed a bug that would sometimes cause an immediate segmentation fault in --sam mode.
  • Fixed script to not omit chromosome 25.
  • Removed -B option from usage message for bowtie-build; that option is not implemented.
  • Fixed issue that could cause Bowtie not to compile when BOWTIE_PTHREADS is left undefined and pthreads.h is not present.
  • Elaborated documentation for -B/--offbase option to indicate that it only affects offsets in the default output mode, not in SAM mode.

Bowtie 2 beta released - 10/16/2011

  • Bowtie 2 2.0.0-beta2 is available now.
  • Differences between Bowtie 2 and Bowtie 1 include:
    • For reads longer than about 50 bp Bowtie 2 is generally faster, more sensitive, and uses less memory than Bowtie 1. For relatively short reads (e.g. less than 50 bp) Bowtie 1 is sometimes faster and/or more sensitive.
    • Bowtie 2 supports gapped alignment with affine gap penalties. Number of gaps and gap lengths are not restricted, except by way of the configurable scoring scheme. Bowtie 1 finds just ungapped alignments.
    • Bowtie 2 supports local alignment, which doesn't require reads to align end-to-end. Local alignments might be "trimmed" ("soft clipped") at one or both extremes in a way that optimizes alignment score. Bowtie 2 also supports end-to-end alignment which, like Bowtie 1, requires that the read align entirely.
    • There is no upper limit on read length in Bowtie 2. Bowtie 1 has an upper limit of around 1000 bp.
    • Bowtie 2 allows alignments to overlap ambiguous characters (e.g. Ns) in the reference. Bowtie 1 does not.
    • Bowtie 2 does away with Bowtie 1's notion of alignment "stratum", and its distinction between "Maq-like" and "end-to-end" modes. In Bowtie 2 all alignments lie along a continuous spectrum of alignment scores where the scoring scheme, similar to Needleman-Wunsch and Smith-Waterman.
    • Bowtie 2's paired-end alignment is more flexible. E.g. for pairs that do not align in a paired fashion, Bowtie 2 attempts to find unpaired alignments for each mate.
    • Bowtie 2 does not align colorspace reads.

Fixed chicken index - 7/19/2011

  • The pre-built chicken genome available from this website was missing chr25. chr25_random was included, but chr25 was erroneously excluded. This is fixed as of today - the index files linked to from the sidebar now contains all chicken chromosomes.

0.12.7 release - 9/7/10

  • Fixes the all-gap reference sequence issue that was present in Bowtie 0.12.6. Index files produced by bowtie-build 0.12.5 and earlier (back to 0.10.*) are compatible with bowtie 0.12.7. Index files produced by bowtie-build 0.12.7 are backward compatible with bowtie 0.12.5 and earlier as long as the first reference sequence is not all-gaps (or, when colorspace indexes, as long as the first reference sequence has two consecutive ACGT characters in it somewhere).
  • Indexes where the first sequence consists of all gaps or other non-ACGT characters are not handled properly by Bowtie versions 0.12.5 and older, but are handled properly by Bowtie 0.12.7.
  • REMOVED: bowtie-build's --old-reverse option; the old reverse- index scheme is again the default. The new scheme is disabled pending further refinement.

0.12.6 release - 8/29/10

  • Modified bowtie-inspect's default mode to use the bit-encoded reference portion of the index to reconstruct the reference sequence, rather than the ebwt portion. This makes bowtie-inspect much faster and uses less memory, and the output for a colorspace index will now be in nucleotide space. To get the behavior of the old default, use the new -e/--ebwt-ref option.
  • Fixed bug whereby SOLiD QV strings without a trailing space would fail to parse.
  • Moved to a new default way of building the reverse index. Revert to the old behavior with bowtie-build's new --old-reverse option. The new reverse index format is forward and backward compatible with `bowtie`, unless otherwise noted in a future version.
  • Fixed issue that would sometimes cause bowtie-build to crash when building a large index with a low --offrate.
  • Fixed build issue that would cause bowtie-build built on one version of Linux to die with a "floating point error" on other versions. bowtie now simply skips reads with 0 characters. Previously it would print an error and exit.
  • Fixed a bug whereby alignment cost could sometimes be miscalculated. Stratum was unaffected.
  • bowtie now simply skips reads with 0 characters. Previously it would print an error and exit.

Myrna paper out - 8/11/10

Myrna released - 7/22/10

  • Myrna is cloud-scale tool for calculating differential gene expression in large RNA-seq datasets. It is very similar to Crossbow in design and philosophy; e.g. it uses Bowtie, it's "tri-mode" (runs in the cloud or on a Hadoop cluster or a single computer), it has a web-form-based GUI for composing and submitting cloud jobs, and its cloud mode uses Elastic MapReduce.

Major update to Crossbow - 7/22/10

  • Crossbow has received a major update to version 1.0.4. New features:

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