Site Map

Latest Release

Related Tools

Pre-built indexes

Publications

Other Documentation

Authors

Links

Recent news

0.12.0 release - Coming soon

• ABI 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".
  • 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.
• bowtie -f now supports fasta files with reads split across multiple lines

Crossbow paper out - 11/20/09

• The provisional version of the Crossbow paper appeared today in Genome Biology.

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

• Crossbow is a cloud-computing pipeline for whole genome resequencing. It combines Bowtie and SoapSNP, an accurate genotyper, on top of Hadoop. Crossbow includes scripts that run automatically on Amazon's EC2 utility computing service for a fee, allowing researchers without extravagant computing resources to conduct large experiments efficiently. Authors are Ben Langmead and Michael C. Schatz.

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.

0.11.0 release - 10/5/09

• Initial SAM output support with -S/--sam option. bowtie sets all fields according to the SAM spec (Version 0.1.2-draft, 20090820). See the new SAM Output section of the manual for details.
• The Getting Started Guide and TUTORIAL file have been updated to use SAMtools instead of Maq for the SNP calling step.
• Added --shmem option: --shmem is similar to --mm in that it allows concurrent bowtie processes querying the same index to share a single memory image of the index. Unlike --mm, shared memory alocated by --shmem is permanent.
• The alignment summary printed to stderr at the end of an alignment run is now more friendly and includes data about the number and proportion of reads that aligned, failed to align, or were suppressed via the -m option.
• When too-short reads are encountered, bowtie now always prints warnings, not errors. --quiet now suppresses those warnings.
• By default, when bowtie prints a reference sequence name it now stops at the first whitespace. In 0.10.1, the default was to print the entire name, which could cause confusion when parsing bowtie output. To revert to printing the full name, use the new --fullref option.
• bowtie now prints the command-line before exiting with an error.
• Fixed mistake in the manual's "Default output" section: the offset in field 4 is 0-based, not 1-based. To obtain a 1-based offset instead, use the -B 1 option.
• Various minor bug fixes.
• Deprecated: -z/--phased, -b/--binout, bowtie-maptool, bowtie-maqconvert. These features will be removed in a future version of Bowtie. Note that -b/--binout, bowtie-maptool, and bowtie-maqconvert are largely superseded by the SAM output format (-S/--sam), BAM, and SAMtools. Contact the authors if this is a problem.
• Removed: --unfq/--unfa/--maxfq/--maxfa/--alfq/--alfa. Please use --un/--max/--al instead. Contact the authors if this is a problem.

Older news