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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

• 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.

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