Published May 17, 2024 | Version v2.5.4
Software Open

BenLangmead/bowtie2: v2.5.4

Creators

  • 1. Johns Hopkins, McKusick-Nathans Institute of Genetic Medicine
  • 2. Johns Hopkins University
  • 3. San Diego Supercomputing Center
  • 4. University of Texas Southwestern Medical Center
  • 5. @TGAC
  • 6. @common-workflow-language
  • 7. @insilicoconsulting
  • 8. @idiv-biodiversity
  • 9. Pendulum Therapeutics
  • 10. @bwlang
  • 11. @10xGenomics
  • 12. Barnab2Studio
  • 13. Yale University
  • 14. @3mdeb
  • 15. GPG
  • 16. Wyoming Public Health Laboratory
  • 17. UCSD - Dept. of Pediatrics
  • 18. @SUSE

Description

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.

Files

BenLangmead/bowtie2-v2.5.4.zip

Files (10.8 MB)

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md5:ed8f73cd85c54d573f1479cde151d77e
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Additional details

Related works

Is supplement to
Software: https://github.com/BenLangmead/bowtie2/tree/v2.5.4 (URL)