Published January 17, 2022
| Version v2.4.5
Software
Open
BenLangmead/bowtie2: Version 2.4.5 - Jan 15, 2022
Creators
- ch4rr0
- val1
- Ben2
- ChristopherWilks
- Daehwan Kim3
- Igor Sfiligoi4
- Nicola Soranzo5
- Jun Aruga
- Christian Brueffer6
- Brad Langhorst7
- ♫ Christian Krause ♫8
- Florian Plaza Oñate9
- Jim10
- Jeff Hussmann11
- Nathan Weeks
- Shaun Jackman12
- Valentin Quiedeville13
- Bernhard M. Wiedemann14
- Daniel McDonald15
- John Marshall
- Marcin Tojek
- Michael R. Crusoe16
- Peter Hickey
- Robert A. Petit III17
- Charles Vejnar18
- 1. Johns Hopkins, McKusick-Nathans Institute of Genetic Medicine
- 2. Johns Hopkins University
- 3. University of Texas Southwestern Medical Center
- 4. San Diego Supercomputing Center
- 5. @TGAC
- 6. SAGA Diagnostics / Lund University
- 7. @bwlang
- 8. @idiv-biodiversity
- 9. INRA MetaGenoPolis
- 10. Whole Biome
- 11. UCSF
- 12. @10xGenomics
- 13. Barnab2Studio
- 14. @SUSE
- 15. UCSD - Dept. of Pediatrics
- 16. @common-workflow-language
- 17. Wyoming Public Health Laboratory
- 18. Yale University
Description
bowtie2
- Fixed issues with
bowtie2
BAM parser that would causebowtie2
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.
- 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 thatbowtie2-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.
- Added a new
-o/--output
option to save the output ofbowtie2-inspect
to a file instead of being dumped to standard output.
Files
BenLangmead/bowtie2-v2.4.5.zip
Files
(10.7 MB)
Name | Size | Download all |
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md5:ab6b5c8da3a339c0d3ca3e62974d3c57
|
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Additional details
Related works
- Is supplement to
- https://github.com/BenLangmead/bowtie2/tree/v2.4.5 (URL)