Issues

• umi_tools dedup is really slow

  CGATOxford/UMI-tools#711 · Filter by author Nitin123-4 opened on Jun 10, 2026
  1

• General Documentation tidy up

  DocumentationNext release
  CGATOxford/UMI-tools#708 · Filter by author IanSudbery opened on May 27, 2026

• Reference Counting (Use-After-Free) Bug for PyList_SetItem

  CGATOxford/UMI-tools#701 · Filter by author wr-web opened on May 4, 2026
  1

• Running umi_tools with barcodes and umi in different fastq files

  CGATOxford/UMI-tools#691 · Filter by author nbbarrientos opened on Jul 21, 2025
  1

• [DOCS] Website issues

  CGATOxford/UMI-tools#685 · Filter by author ns-rse opened on Apr 28, 2025

• grouping by cell barcode and adding cell barcode tag to bams

  CGATOxford/UMI-tools#684 · Filter by author JNWorkman opened on Apr 25, 2025
  1

• Combining --cell-tag with --extract-umi-method=read_id

  CGATOxford/UMI-tools#682 · Filter by author yaccos opened on Apr 23, 2025
  6

• How to Generate a UMI Whitelist from a String List Using umitools?

  CGATOxford/UMI-tools#681 · Filter by author DC-Jade opened on Apr 14, 2025
  7

• UMIs on header

  CGATOxford/UMI-tools#680 · Filter by author RTCarmo opened on Mar 10, 2025
  3

• using regex gives empty file

  CGATOxford/UMI-tools#674 · Filter by author dewshr opened on Jan 22, 2025
  4

• Killed process dedup

  CGATOxford/UMI-tools#671 · Filter by author denise0593 opened on Nov 25, 2024
  3

• Documentation for prepare-for-rsem.

  CGATOxford/UMI-tools#670 · Filter by author IanSudbery opened on Nov 17, 2024
  2

• No v1.1.6 on conda, and only prebuilt for MacOS (no source) on pypi

  CGATOxford/UMI-tools#663 · Filter by author eachanjohnson opened on Oct 9, 2024
  3

• Issue with group and dedup option

  CGATOxford/UMI-tools#660 · Filter by author LioLenr opened on Aug 20, 2024

• Documentation improvement suggestion

  Documentation
  CGATOxford/UMI-tools#648 · Filter by author hazmup opened on May 31, 2024
  2

  

• UMI-tool 1.1.5 not working with --per-gene --per-contig --gene-transcript-map

  Next release
  CGATOxford/UMI-tools#646 · Filter by author pclavell opened on May 31, 2024
  6

  

• provide an explicit list of cell barcodes to whitelist?

  Next release
  CGATOxford/UMI-tools#642 · Filter by author bbimber opened on May 7, 2024
  5

• group method: not all UMI-containing reads assigned UG tag

  Documentation
  CGATOxford/UMI-tools#635 · Filter by author epiliper opened on Mar 20, 2024
  7

  

• Dedup errors if input BAM file is empty

  Next release
  CGATOxford/UMI-tools#624 · Filter by author IanSudbery opened on Jan 24, 2024
  2

• Documenting algorithms

  Documentation
  CGATOxford/UMI-tools#423 · Filter by author TomSmithCGAT opened on Jul 13, 2020
  

• umi_tools dedup: Incorrect output with using --paired

  CGATOxford/UMI-tools#347 · Filter by author christianbioinf opened on Jul 5, 2019
  10

• Parallel deduplication

  CGATOxford/UMI-tools#203 · Filter by author TomSmithCGAT opened on Oct 19, 2017
  5

  

• Abstract core algorithm in to C library

  enhancement
  CGATOxford/UMI-tools#96 · Filter by author IanSudbery opened on Mar 20, 2017
  17