v2.5.4

bowtie2

• Added --sam-opt-config command line option for toggling SAM Opt flags.
  See MANUAL for details.
• Fixed an issue causing bowtie2's memory usage to increase over time
  when aligning BAM files.
• Changed bowtie2 to continue flushing output in the event of a partial write.
• Changed the behavior of bowtie2-build to throw an exception if it is unable
  to write the BWT (.1.bt2, .1.rev.bt2). In prior versions bowtie2-build, would silently
  ignore the error which has led some to report the absence of the BWT files in
  a "completed" index build.
• Reverted the changes made in v2.5.0 that sometimes caused unique concordant alignments to be over-counted.

v2.5.3

Version 2.5.3 - Jan 16, 2024

• Fixed an issue causing bowtie2's memory usage to increase over time.
• Fixed an issue causing bowtie2 to crash when processing empty FASTQ records.
• Fixed an issue that would cause bowtie2 to erroneously treat -f and -F as mutually exclusive.
• Add optional support for libsais to bowtie2-build for faster index building.
  N.B. -- small indexes are capped at 2GB when using libsais as opposed to 4GB when using the
  default blockwise algorithm. See MANUAL for more details.

v2.5.2

• Fixed an issue preventing bowtie2 from utilizing the specified number of CPU cores
• Fixed an issue causing bowtie2 to segfault when reading compressed inputs on Windows
• Fixed an issue causing bowtie2 to segfault while parsing interleaved reads
• Overhauled the FASTQ parser with better tolerance for empty lines

v2.5.1

• Fixed an issue affecting bowtie2 alignment accuracy.
• Updated the versions of the NCBI NGS and VDB libraries used by bowtie2.
• Fixed a segmentation fault that would occur while aligning SRA data.
• Fixed an issue preventing --un-mates from properly saving unaligned mates.

Update
02/28/2023 - Added SRA package for MacOS x86-64

v2.5.0

• Overall improvements in the use of prefetch instructions. (contribution by Igor Sfiligoi)
• Made input/output fully asynchronous by using a dedicated thread. (contribution by Igor Sfiligoi)
• Added support for AVX2 256-bit instructions with can be enabled by
  setting the SSE_AXV2 environment variable at compile time. (contribution by Igor Sfiligoi)
• Fixed an issue causing bowtie2 to crash when processing ZSTD
  files with high compression ratios.
• Changed the way that unique alignments are counted in summary
  message to better match up with filters on SAM output

Version 2.4.5 - Jan 15, 2022

bowtie2

• Fixed issues with bowtie2 BAM parser that would cause bowtie2 to
  crash when processing input that was encoded with tools other than
  samtools e.g. Picard.
• Fixed an issue causing bowtie2 to drop certain optional fields when
  when aligning BAM reads with the --preserve-tags option.
• Fixed an issue causing bowtie2 to produce mangled SAM output when
  specifying --sam-append-comment together with the --passthrough
  option.
• Appended GO:query to SAM @HD entry to indicate that reads are
  grouped by query name, bump SAM version to 1.5 to indicate support
  for this change.

bowtie2-build

• Implemented thread pool to address performance regressions
  introduced during the switch to C++11 threads.
• Fixed an issue causing masked-sequence metadata to be omitted
  from index. This issue would subsequently result in sequence
  data, @SQ, being left out from alignment SAM header.
• Included .tmp extension to index files currenlty being built.
  The extension is removed only upon successful build. This change
  seeks to address the assumption that bowtie2-build ran successfully
  without building the reverse indexes.
• Fixed an issue causing bowtie2-build to sometimes incorrectly
  calculate input size. This issue would result in the wrong index type
  being chosen and only happened with GZip compressed files.

bowtie2-inspect

• Added a new -o/--output option to save the output of
  bowtie2-inspect to a file instead of being dumped to standard
  output.

v2.4.4

• Fixed an issue that would sometimes cause deadlocks in bowtie2 when running multithreaded

v2.4.3

* Replaced TBB concurrency with C++ threads
* Added native support for processing Zstd-compressed read files
  to bowtie2
* Added native support for processing Zstd-compressed
  reference-genome files to bowtie2-build
* Fixed an issue causing `bowtie2` to report incorrect alignments
  on big-endian machines
* Fixed an issue causing `bowtie2` to incorrectly process BAM
  files on big-endian machines
* Fixed an issue causing Bowtie2 to set an incorrect MAPQ when AS and
  XS are the maximum for read length
* Add support for building on Apple M1 processors

v2.4.2

* Fixed an issue that would cause the `bowtie2` wrapper script to throw
  an error when using wrapper-specific arguments.
* Added new `--sam-append-comment` flag that appends comment from FASTA/Q
  read to corresponding SAM record.
* Fixed an issue that would cause qupto, `-u`, to overflow when there
  are >= 2^32 query sequences (PR #312).
* Fixed an issue that would cause bowtie2-build script to incorrectly
  process reference files.

v.2.4.1

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