Published October 3, 2024 | Version v1.1.6
Software Open

CGATOxford/UMI-tools: v1.1.6

  • 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

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