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, NCBI GRCh38 2.7 GB
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, 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, NCBI v37 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
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.



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1.2.0 - 12/12/2016

This is a major release with some larger and many smaller changes. These notes emphasize the large changes. See commit history for details.

  • Code related to read parsing was completely rewritten to improve scalability to many threads. In short, the critical section is simpler and parses input reads in batches rather than one at a time. The improvement applies to all read formats.
  • --reads-per-batch command line parameter added to specify the number of reads to read from the input file at once
  • TBB is now the default threading library. We consistently found TBB to give superior thread scaling. It is widely available and widely installed. That said, we are also preserving a "legacy" version of Bowtie that, like previous releases, does not use TBB. To compile Bowtie source in legacy mode use NO_TBB=1. To use legacy binaries, download the appropriate binary archive with "legacy" in the name.
  • Bowtie now uses a queue-based lock rather than a spin or heavyweight lock. We find this gives superior thread scaling; we saw an order-of-magnitude throughput improvements at 120 threads in one experiment, for example.
  • Unnecessary thread synchronization removed
  • Fixed colorspace parsing when primer base is present
  • Fixed bugs related to --skip command line option

1.1.2 - 6/23/2015

  • Fixed the building process for Mac OS X Yosemite.
  • Added install target (make install) for Linux to better aid package building process and the overall installation process.
  • Added support for Intel TBB threading, providing better thread scaling in most situations. The default build still uses TinyThread but TBB is used with make WITH_TBB=1.
  • Fixed minor issue related with managing the number of threads spawned.
  • Fixed minor issue which may have caused a memory leak after an exception was thrown.
  • Fixed bug that caused bowtie to crash if a read was trimmed more than the read's length on 5' end.
  • Added minor corrections/addition to the manual.
  • Fixed bug that caused the wrapper to incorrectly identify the bowtie binary.

Lighter released

  • Lighter is an extremely fast and memory-efficient program for correcting sequencing errors in DNA sequencing data. For details on how error correction can help improve the speed and accuracy of downstream analysis tools, see the paper in Genome Biology. Source and software available at GitHub.

1.1.1 - 10/1/2014

  • Fixed a compiling linkage problem related with Mac OS X Mavericks.
  • Improved performance for cases where the reference contains many stretches of 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.

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