|Bowtie: Ultrafast short read alignment|
|Crossbow: Genotyping, cloud computing|
|Myrna: Cloud, differential gene expression|
|Tophat: RNA-Seq splice junction mapper|
|Cufflinks: Isoform assembly, quantitation|
|Lighter: Fast error correction|
|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)|
|H. sapiens, NCBI GRCh38||3.5 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.
- Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012, 9:357-359.
- 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.
Version 2.3.1 - Mar 03, 2017
Please note that as of this release Bowtie 2 now has dependencies on zlib and readline libraries. Make sure that all dependencies are met before attempting to build from source.
- Added native support for gzipped read files. The wrapper script is no longer responsible for decompression. This simplifies the wrapper and improves speed and thread scalability for gzipped inputs.
- Fixed a bug that caused 'bowtie2-build' to crash when the first FASTA sequence contains all Ns.
- Add support for interleaved FASTQ format -—interleaved.
- Empty FASTQ inputs would yield an error in Bowtie 2 2.3.0, whereas previous versions would simply align 0 reads and report the SAM header as usual. This version returns to the pre-2.3.0 behavior, resolving a compatibility issue between TopHat2 and Bowtie 2 2.3.0.
- Fixed a bug whereby combining -—un-conc* with -k or -a would cause 'bowtie2' to print duplicate reads in one or both of the --un-conc* output files, causing the ends to be misaligned.
- The default ---score-min for --local mode is now 'G,20,8'. That was the stated default in the documentation for a while, but the actual default was 'G,0,10' for many versions. Now the default matches the documentation and, we find, yields more accurate alignments than 'G,0,10'
Version 2.3.0 - Dec 13, 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.
- 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 issue with parsing FASTA records with greater-than symbol in the name
- Now detects and reports inconsistencies between --score-min and --ma
- Changed default for --bmaxdivn to yield better memory footprint and running time when building an index with many threads
Bowtie2 developers note
As of Nov 2015 we had to fix the bowtie2 github repo and relabel the entire history. Developers and contributors should re-clone the bowtie2 github repo from this current state.
Version 2.2.9 - Apr 22, 2016
- Fixed the multiple threads issue for the bowtie2-build.
- Fixed a TBB related build issue impacting TBB v4.4.
Version 2.2.8 - Mar 10, 2016
- Various website updates.
- Fixed the bowtie2-build issue that made TBB compilation fail.
- Fixed the static build for Win32 platform.
Version 2.2.7 - Feb 10, 2016
- Added a parallel index build option: bowtie2-build --threads <# threads>.
- Fixed an issue whereby IUPAC codes (other than A/C/G/T/N) in reads were converted to As. Now all non-A/C/G/T characters in reads become Ns.
- Fixed some compilation issues, including for the Intel C++ Compiler.
- Removed debugging code that could impede performance for many alignment threads.
- Fixed a few typos in documentation.
Version 2.2.6 - Jul 22, 2015
- Switched to a stable sort to avoid some potential reproducibility confusions.
- Added 'install' target for *nix platforms.
- Added the Intel TBB option which provides in most situations a better performance output. TBB is not present by default in the current build but can be added by compiling the source code with WITH_TBB=1 option.
- Fixed a bug that caused seed lenght to be dependent of the -L and -N parameters order.
- Fixed a bug that caused --local followed by -N to reset seed lenght to 22 which is actually the default value for global.
- Enable compilation on FreeBDS and clang, although gmake port is still required.
- Fixed an issue that made bowtie2 compilation process to fail on Snow Leopard.
Version 2.2.5 - Mar 9, 2015
- Fixed some situations where incorrectly we could detect a Mavericks platform.
- Fixed some manual issues including some HTML bad formating.
- Make sure the wrapper correctly identifies the platform under OSX.
- Fixed --rg/--rg-id options where included spaces were incorrectly treated.
- Various documentation fixes added by contributors.
- Fixed the incorrect behavior where parameter file names may contain spaces.
- Fixed bugs related with the presence of spaces in the path where bowtie binaries are stored.
- Improved exception handling for missformated quality values.
- Improved redundancy checks by correctly account for soft clipping.