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Version 2.4.1 - Feb 28, 2020

• Fixed an issue that would cause the bowtie2 wrapper script to incorrectly process certain arguments

Version 2.4.0 - Feb 25, 2020

• Fixed an issue in -b <bam> input mode where one might prematurely close the read file pointer causing “Bad file descriptor” in other threads
• Fixed an issue that could cause bowtie2 to crash in --no-1mm-upfront mode
• Modified bowtie2-build to better handle of flags and positional parameters
• Migrated all python scripts to python3
• Added support for wildcards in input files to bowtie2, e.g. bowtie2 -x index -q *.fq as opposed to bowtie2 -x index -q 1.fq,2.fq,3.fq...
• Fixed an issue causing bowtie2 to incorrectly process read names with slash mates plus extra characters (see #265)
• Clarified support for overriding presets with more specific options e.g bowtie2 -x index --local --very-fast-local --L22 -q reads.fq will set the seed length to 22, overriding the 25 set by --very-fast-local
• Modified SAM output for -k/-a so that supplementary alignments get assigned a MAPQ of 255
• Fixed an issue that would sometimes cause bowtie2-build to not generate reverse index files
• Added preliminary support for ppc64le architectures with the help of SIMDE project (see #271)
• Fixed an issue causing bowtie2 to incorrectly calculate the MAPQ when --mp was specified in combination with --ignore-quals

1000-Genomes major-allele SNP references -- April 26, 2019

• For each base where the typical reference has the non-majority allele (according to the 1000 Genomes Project, we substituted in the majority allele instead
• Links for indexes added to sidebar, as are links for the edited FASTA files
• We made versions both for GRCh38 primary assembly and hg19 assembly
• See how we created them
• Only SNPs (single-base substitutions) are considered for now; indels are future work
• Because only SNPs are considered, coordinates (e.g. gene annotations) are the same as for typical GRCh38 and hg19 assemblies. Most downstream tools are unaffected as long as major-allele-edited FASTAs are used wherever genome sequences are required.

Version 2.3.5.1 - April 16, 2019

• Added official support for BAM input files
• Added official support for CMake build system
• Added changes to Makefile for creating Reproducible builds (via #210)
• Fix an issue whereby building on aarch64 would require patching sed commands (via #243)
• Fix an issue whereby bowtie2 would incorrectly throw an error while processing --interleaved input

Version 2.3.5 - March 16, 2019

Check out the Bowtie 2 UI, currently in beta, a shiny, frontend to the Bowtie2 command line.

• Added support for obtaining input reads directly from the Sequence Read Archive, via NCBI’s NGS language bindings. This is activated via the --sra-acc option. This implementation is based on Daehwan Kim’s in HISAT2. Supports both unpaired and paired-end inputs.
• Bowtie 2 now compiles on ARM architectures (via #216)
• --interleaved can now be combined with FASTA inputs (worked only with FASTQ before)
• Fixed issue whereby large indexes were not successfully found in the $BOWTIE2_INDEXES directory
• Fixed input from FIFOs (e.g. via process substitution) to distinguish gzip-compressed versus uncompressed input
• Fixed issue whereby arguments containing bz2 lz4 were misinterpretted as files
• Fixed several compiler warnings
• Fixed issue whereby both ends of a paired-end read could have negative TLEN if they exactly coincided
• Fixed issue whereby bowtie2-build would hang on end-of-file (via #228)
• Fixed issue whereby wrapper script would sometimes create zombie processes (via #51)
• Fixed issue whereby bowtie2-build and bowtie2-inspect wrappers would fail on some versions of Python/PyPy
• Replaced old, unhelpful README.md in the project with a version that includes badges, links and some highlights from the manual
• Note: BAM input support and CMake build support both remain experimental, but we expect to finalize them in the next release

Version 2.3.4.3 - September 17, 2018

• Fixed an issue causing bowtie2-build and bowtie2-inspect to output incomplete help text.
• Fixed an issue causing bowtie2-align to crash.
• Fixed an issue preventing bowtie2 from processing paired and/or unpaired FASTQ reads together with interleaved FASTQ reads.

Version 2.3.4.2 - August 07, 2018

• Fixed issue causing bowtie2 to fail in --fast-local mode.
• Fixed issue causing --soft-clipped-unmapped-tlen to be a positional argument.
• New option --trim-to N causes bowtie2 to trim reads longer than N bases to exactly N bases. Can trim from either 3' or 5' end, e.g. --trim-to 5:30 trims reads to 30 bases, truncating at the 5' end.
• Updated "Building from source" manual section with additional instructions on installing TBB.
• Several other updates to manual, including new mentions of Bioconda and Biocontainers.
• Fixed an issue preventing bowtie2 from processing more than one pattern source when running single threaded.
• Fixed an issue causing bowtie2 and bowtie2-inspect to crash if the index contains a gap-only segment.
• Added experimental BAM input mode -b. Works only with unpaired input reads and BAM files that are sorted by read name (samtools sort -n). BAM input mode also supports the following options:
•     --preserve-sam-tags: Preserve any optional fields present in BAM record
    --align-paired-reads: Paired-end mode for BAM files
• Add experimental CMake support

Thread-scaling paper appears - July 19, 2018

• Our latest work on Bowtie's core thread scaling capabilities just appeared Open Access in the journal Bioinformatics

Version 2.3.4.1 - February 03, 2018

• Fixed an issue with --reorder that caused bowtie2 to crash while reordering SAM output

Version 2.3.4 - December 29, 2017

• Fixed major issue causing corrupt SAM output when using many threads (-p/--threads) on certain systems.
• Fixed an issue whereby bowtie2 processes could overwrite each others' named pipes on HPC systems.
• Fixed an issue causing bowtie2-build and bowtie2-inspect to return prematurely on Windows.
• Fixed issues raised by compiler "sanitizers" that could potentially have caused memory corruption or undefined behavior.
• Added the "continuous FASTA" input format (-F) for aligning all the k-mers in the sequences of a FASTA file. Useful for determining mapability of regions of the genome, and similar tasks.

Version 2.3.3.1 - October 05, 2017

• Fixed an issue causing input files to be skipped when running multi-threaded alignment
• Fixed an issue causing the first character of a read name to be dropped while parsing reads split across multiple input files

Version 2.3.3 - September 06, 2017

From this release forward prepackaged bowtie2 binaries are now statically linked to the zlib compression library and, the recommended threading library, TBB. Users who rely on prepackaged builds are no longer required to have these packages pre-installed. As a result of the aforementioned changes legacy packages have been discontinued.

• bowtie2-build now supports gzip-compressed FASTA inputs
• New --xeq parameter for bowtie2 disambiguates the 'M' CIGAR flag. When specified, matches are indicated with the = operation and mismatches with X
• Fixed a possible infinite loop during parallel index building due to the compiler optimizing away a loop condition
• Added --soft-clipped-unmapped-tlen parameter for bowtie2 that ignores soft-clipped bases when calculating template length (TLEN)
• Added support for multi-line sequences in FASTA read inputs
• Expanded explanation of MD:Z field in manual
• Fixed a crashing bug when output is redirected to a pipe
• Fixed ambiguity in the SEED alignment policy that sometimes caused -N parameter to be ignored

Version 2.3.2 - May 05, 2017

• Now reports MREVERSE SAM flag for unaligned end when only one end of a pair aligns
• Fixed issue where first character of some read names was omitted from SAM output when using tabbed input formats
• Added --sam-no-qname-trunc option, which causes entire read name, including spaces, to be written to SAM output. This violates SAM specification, but can be useful in applications that immediately postprocess the SAM.
• Fixed compilation error caused by pointer comparison issue in aligner_result.cpp
• Removed termcap and readline dependencies introduced in v2.3.1
• Fixed compilation issues caused by gzbuffer function when compiling with zlib v1.2.3.5 and earlier. Users compiling against these libraries will use the zlib default buffer size of 8Kb when decompressing read files.
• Fixed issue that would cause Bowtie 2 hang when aligning FASTA inputs with more than one thread