Bowtie

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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Related Tools

    Crossbow: Genotyping, cloud computing
    Tophat: RNA-Seq splice junction mapper
    Cufflinks: Isoform assembly, quantitation

Pre-built 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 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
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.

Pre-built indexes are compatible with Bowtie versions 0.9.8 and later. For older indexes, please contact us.

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Other Documentation

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Recent news

0.12.2 release - 2/2/10

  • When -C/--color is enabled, the default paired-end orientation is now --ff, not --fr. The new default fits typical SOLiD output.
  • Fixed a bug whereby very large reads could cause bowtie to crash in --best mode
  • After 0.12.1, some issues remained whereby bowtie would fail to trim the primer in colorspace (e.g. in -c mode). All input modes should now have fully-functioning colorspace primer trimming.
  • Fixed a bug whereby decoded colorspace qualities could overflow and erroneously become low qualities.
  • Fixed a bug that could produce incorrect paired-end alignment results in -n mode when using paired-end orientation modes other than --fr Even with the bug, reported results are reasonable; but the seed edit constraint ( -n ) may have been applied to the wrong end of one of the mates.
  • Changed --chunkmbs default up to 64 from 32.
  • Better error checking and reporting for some bowtie options.
  • Some basic testing scripts are now bundled with Bowtie (in scripts/test), which should make it easier to regression-test.

Fixed mm9 colorspace index

  • Previously posted version of the colorspace mm9 index was not actually colorspace. This has been fixed.

0.12.1 release - 1/8/10

  • IMPORTANT: Fixed bug whereby bowtie would fail to remove both the primer base and the first color when parsing .csfasta files with primer bases in -C -f mode. A workaround for users of version 0.12.0 is to use -5 1 in that situation.
  • Fixed bug whereby, when -M limit was exceeded for an unpaired read, the number output in the 7th column (or the XM:i optional field) for the randomly-selected alignment was too low by 1.
  • Added discussion to manual about a pitfall regarding SOLiD paired-end input, i.e., not all entries necessarily have corresponding mates in the other file.

0.12.0 release - 12/23/09

  • Added missing README.markdown file
  • Minor documentation additions

0.12.0-beta1 release - 12/15/09

  • Added SOLiD colorspace support
    • Colorspace indexes are distinct from standard letterspace indexes and must be built with a separate invocation of bowtie-build (with -C option)
    • Running bowtie with -C causes Bowtie to align in colorspace. Both index and reads must be in colorspace.
    • Colorspace memory requirement is the same as paired-end alignment in letterspace (normal) mode. Paired-end alignment does not increase the memory requirement further in colorspace.
    • csfasta, csfastq, and "raw" read formats are all supported with -C. In read sequences, 0 means "blue" and is intechangeable with A, likewise 1 (C) means "green", 2 (G) means "orange" and 3 (T) means "red".
    • Colorspace versions of indexes added (see sidebar)
    • New manual section discussing colorspace features
  • Fixed a few SAM output issues
    • @PG line now properly uses colons instead of equals signs
    • Removed /1, /2 suffixes for paired-end reads in SAM mode
    • Added --sam-RG option that permits the user to insert set values for flags that appear on the @RG line
  • Fixed lingering pthreads bugs that could cause Bowtie to hang or crash toward the end of execution with -p > 1.
  • Fixed performance-related bug that would cause paired-end alignment to be artificially slow in many situations.
  • Fixed issue with random number generation that would result in non-random selection of alignments in some situations.
  • bowtie -f now supports fasta files with reads split across multiple lines
  • New --suppress option suppresses unwanted columns of output
  • The MANUAL file was converted to markdown format, facilitating conversion to various other formats using tools like pandoc
  • Deprecated: bowtie: --concise, bowtie-build: --big, --little
  • Removed: -z/--phased, -b/--binout, bowtie-maptool, bowtie-maqconvert

Crossbow paper out - 11/20/09

New pre-built index list - 11/14/09

  • The roster of pre-built indexes has been changed to address a number of user requests and issues and to streamline maintenance. Now:
    • All indexes are for well known assemblies. Contig indexes have been removed.
    • Indexes for UCSC builds hg18, hg19 and mm9 have been added.
    • Rarely used indexes (chimp, rat, dog, chicken) have been removed.
  • If there is an index not on the list that you use on a regular basis and would like to be made availble pre-built, contact us. We may add more if enough users request them.
  • Note: neither UCSC nor NCBI indexes contain unplaced contigs (UCSC: "random" files, NCBI: Chromosome "Un") or alternative haplotype assemblies.

Bowtie on Galaxy - 10/15/09

  • The Galaxy project has integrated Bowtie as one of the tools available for aligning short reads (under "NGS: Mapping" on in the "Tools" box). Many thanks to Anton Nekrutenko for his work on that.

0.11.3 release - 10/12/09

  • Fixed crashing bug in -S/--sam mode when the number of reference sequences in the index is very large.
  • Added --sam-nohead option to suppress output of SAM headers in -S/--sam mode.
  • Added --sam-nosq option to suppress output of @SQ SAM headers in -S/--sam mode. These can become a nuisance when the reference index contains a very large number of sequences.
  • Fixed a bug in bowtie-build's auto-configure mode that would cause it to underestimate the amount of memory required by a set of parameters. This in turn would cause the index to be corrupted.

Crossbow released - 10/9/09

0.11.2 release - 10/7/09

  • Fixed issue whereby --max option was disabled.

0.11.1 mini-release - 10/5/09

  • SAM output: changed XS:i optional field to be named XA:i to avoid a conflict with TopHat's XS:i field.

Older news