/bowtie2

Latest release

v2.3.2

@ch4rr0 ch4rr0 released this May 6, 2017 · 5 commits to master since this release

  • Added support for interleaved paired-end FASTQ inputs (--interleaved)
  • 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

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v2.3.0

@ch4rr0 ch4rr0 released this Dec 30, 2016 · 873 commits to master since this release

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

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Release 2.2.9

@val-antonescu val-antonescu released this Apr 21, 2016 · 1014 commits to master since this release

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.

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Release 2.2.8

@val-antonescu val-antonescu released this Mar 10, 2016 · 1020 commits to master since this release

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.

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Release 2.2.7

@val-antonescu val-antonescu released this Feb 12, 2016 · 1050 commits to master since this release

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.

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