All pull requests

Pull requests

• Coverage normalization at gene level and visualisation of diverging layers (#2661, #2674)

  #2876·AviHuene opened Oct 30, 2026Contributor·6 tasks·

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• anvi-profile: --skip-SNV-storage and --min-indel-length for long-read indel surveys

  #2874·Ge0rges opened Oct 28, 2026Collaborator·

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• Discov version 2

  #2872·ivagljiva opened Oct 28, 2026Contributor·5 tasks·

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• anvi-profile: record a deletion that crosses a split boundary once, whole

  #2871·Ge0rges opened Oct 28, 2026Collaborator·

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• Add 'num reads mapped' tables to profile database

  migrationprofile database
  #2870·ivagljiva opened Oct 27, 2026Contributor·

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• Remove --manual-mode, a historical artifact

  #2868·meren opened Oct 26, 2026Member·

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• Use pyANI-plus for ANIb and ANIm on Python 3.13

  #2845·bcoltman opened Oct 5, 2026Contributor·

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• Move the supported runtime to Python 3.13 and Snakemake 9

  #2842·bcoltman opened Oct 5, 2026Contributor·

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• Fix workflow table parsing and mapped-read import reruns

  #2840·bcoltman opened Oct 5, 2026Contributor·

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• Update pandas APIs and preserve missing-value handling

  #2838·bcoltman opened Oct 5, 2026Contributor·

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• Correct gene coverage mask decoding and INSEQ recovery

  #2837·bcoltman opened Oct 5, 2026Contributor·

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• Fix split-FASTA test output paths and invalid escape sequences

  #2833·bcoltman opened Oct 5, 2026Contributor·

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• Add help page for pangenomics workflow

  #2807·ivagljiva opened Sep 10, 2026Contributor·

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• Add anvi-export-genome-specific-trna-modifications

  #2719·tucker4 opened Jun 8, 2026Contributor·

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• Enable metabolism framework tests

  #2713·ulgens opened Jun 7, 2026Collaborator·

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• Lazy snv access

  #2691·FlorianTrigodet opened May 28, 2026Contributor·

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• Port anvi'o to Python 3.13

  #2681·bcoltman opened May 24, 2026Contributor·

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• anvi-report-indels: track mobile indels

  hackathon 2026
  #2673·FlorianTrigodet opened May 22, 2026Contributor·

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• Add anvi-screw-you: It empathizes with the user once they are frustrated

  hackathon 2026
  #2671·sarilog opened May 22, 2026Contributor·

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• Add modifications parsing from MM and ML tags in BAMs during anvi-profile

  hackathon 2026
  #2663·Ge0rges opened May 21, 2026Collaborator·

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• Add first-class PHROGs support via anvi-setup-phrogs and anvi-run-phrogs

  hackathon 2026
  #2649·Ge0rges with CopilotAI opened May 20, 2026·

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• Profile read clipping events from BAM files

  hackathon 2026
  #2645·FlorianTrigodet opened May 20, 2026Contributor·

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• General implementation for annotation with user-defined databases

  hackathon 2026
  #2644·l-gallucci opened May 20, 2026Contributor·

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• anvi-compute-functional-consensus: *FunctionalConsensus classes

  hackathon 2026
  #2633·ChiaraVanni opened May 20, 2026Contributor·

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• Python 3.14 support

  #2628·ulgens opened May 20, 2026Collaborator·

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