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- Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.
- For release updates, subscribe to the mailing list.
| Bowtie 0.12.8 | 5/6/12 |
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Pre-built indexes
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.
Publications
- Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.
- Langmead B, Schatz M, Lin J, Pop M, Salzberg SL. Searching for SNPs with cloud computing. Genome Biology 10:R134.
- Trapnell C, Pachter L, Salzberg SL, TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009 25(9):1105-1111.
Other Documentation
Authors
Links
Recent news
0.12.8 release - 5/6/12
- Fixed a bug that would sometimes cause an immediate segmentation fault in --sam mode.
- Fixed make_galGal3.sh 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:
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- 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
- The provisional version of the Myrna paper appeared today in Genome Biology. See the Myrna site for details about the software.
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:
- New "tri-mode" design; Crossbow jobs can be run in the cloud (on Amazon AWS), on a Hadoop cluster, or on a single computer, exploiting multiple processor cores
- Added a web-form-based GUI for composing and submitting cloud jobs.
- Cloud version of Crossbow now runs on Elastic MapReduce (EMR) rather than directly on Elastic Compute Cloud (EC2).
Cufflinks paper out - 5/3/10
- The Cufflinks paper, by Cole Trapnell et al is out in Nature Biotechnology. See the supplement for a detailed discussion of the methods behind Cufflinks.
0.12.5 release - 4/10/10
- Fixed spurious "Error while writing string output; not all characters written" errors in -S/--sam mode.
0.12.4 release - 4/5/10
- Periods in read sequences are now treated as Ns instead of ignored. This should help with some problems where Bowtie erroneously reports "Reads file contained a pattern with more than 1024 quality values..." for data from recent versions of the Illumina GA pipeline.
- Fixed a bug whereby some error and warning messages would be printed on top of each other in -p/--threads mode.
- Chunk-exhaustion warnings messages are now suppressed when --quiet is specified.
- Fixed small issue in quality decoding whereby no-confidence colors would incorrectly influence decoded quality of adjacent bases.
0.12.3 release - 2/17/10
- Fixed a significant bug in -C/--color mode whereby quality values for SNP nucleotide positions are erroneously penalized.
- Fixed a bug in -S/--sam mode whereby if whitespace occurred in the original read name, it would be printed in the QNAME field in violation of the SAM spec. Bowtie now truncates read names at the first whitespace character before printing.
- When input is FASTQ and -C/--color is enabled, Bowtie is now tolerant of output from FASTQ converters that include the primer base and where the quality string is one character shorter than the sequence string (due to the primer). This fixes issues users have reported using output from BFAST's solid2fastq.
- Added support for SOLiD-style _QV files, via the -Q/--quals, --Q1 and --Q2 options. These options are used in combination with -C/--color and -f to align parallel colorspace read/quality files without having to convert to FASTQ.
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.
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