CGATOxford/UMI-tools: v1.1.6
Creators
- Tom Smith
- Ian Sudbery1
- Chang Y
- Michael Jackson2
- Peter Chovanec
- Jesse Bloom3
- jz314
- Eachan Johnson4
- Johannes Köster5
- Matt Stone6
- Simon P Shen7
- Yu Fu8
- akmorrow13
- Bo Han
- cui jie
- Kohl Kinning9
- rajivnarayan
- Michael Strasser
- Jan Oppelt10
- James Oguya
- Patrick Roelli
- Elmar Pruesse
- Daniel Liu
- christianbioinf
- Christian Brueffer11
- Avi Srivastava12
- Andreas Heger13
- 1. University of Sheffield
- 2. EPCC, The University of Edinburgh
- 3. Fred Hutchinson Cancer Research Center; Howard Hughes Medical Institute
- 4. @FrancisCrickInstitute
- 5. University of Duisburg-Essen
- 6. @fulcrumgenomics
- 7. @Harvard
- 8. Boston University
- 9. University of Colorado Anschutz Medical Campus
- 10. St. Anna CCRI
- 11. @insilicoconsulting
- 12. The Wistar Institute
- 13. MRC
Description
UMI-tools output is now deterministic with --random-seed
Many users have had issues with making UMI-tools deterministic, which previously relied upon both --random-seed
and the enivornmental variable PYTHONHASHSEED
being set. From v1.1.6
only --random seed
is required.
Please note that in some cases the implemented solution may make the output from v.1.1.6 different to previous versions, even if --random-seed
is set to the same value. The differences will be very slight and the different outputs represent equally sensible UMI grouping/deduplication since they relate only to how ties are broken.
Thank you @TyberiusPrime, @christianbioinf and others for their suggestions for how to remove the dependency on PYTHONHASHSEED
for deterministic output.
New features
- umi_tools is now deterministic when using --random-seed - @TomSmithCGAT in https://github.com/CGATOxford/UMI-tools/pull/550
- Option to extract barcode from read2 only - @TomSmithCGAT in https://github.com/CGATOxford/UMI-tools/pull/630
- Adds support for python 3.12 - @IanSudbery in https://github.com/CGATOxford/UMI-tools/pull/657
Bugfix
- Avoids switching matplotlib backend - @sshen8 in https://github.com/CGATOxford/UMI-tools/pull/640
- count_tab now correctly reads UMI and cell barcodes - @eachanjohnson in https://github.com/CGATOxford/UMI-tools/pull/654
- count_tab now writes out strings not bytes - @eachanjohnson in https://github.com/CGATOxford/UMI-tools/pull/654
- Installation with < python 3 prevented - @IanSudbery in https://github.com/CGATOxford/UMI-tools/pull/644
Documentation
- FAQ entry regarding identification of possible duplicates reads/pairs - @TomSmithCGAT in https://github.com/CGATOxford/UMI-tools/pull/631
- Improved docs regarding chimeric/unmapped/unpaired read pairs - @TomSmithCGAT in https://github.com/CGATOxford/UMI-tools/pull/629
Other
- Add issue templates - @TomSmithCGAT in https://github.com/CGATOxford/UMI-tools/pull/632
- Update testing suite to pytest - @eachanjohnson in https://github.com/CGATOxford/UMI-tools/pull/655
New Contributors
- @sshen8 made their first contribution in https://github.com/CGATOxford/UMI-tools/pull/640
- @eachanjohnson made their first contribution in https://github.com/CGATOxford/UMI-tools/pull/654
Full Changelog: https://github.com/CGATOxford/UMI-tools/compare/1.1.5...v1.1.6
Files
CGATOxford/UMI-tools-v1.1.6.zip
Files
(16.9 MB)
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Additional details
Related works
- Is supplement to
- Software: https://github.com/CGATOxford/UMI-tools/tree/v1.1.6 (URL)