Issues

• [question] Question about Lighter being used twice

  question
  bactopia/bactopia#683 · Filter by author abomba opened on Sep 25, 2026

• [feature]

  enhancement
  bactopia/bactopia#681 · Filter by author Gabriella-Veytsel opened on Sep 22, 2026

• [bug] Cannot use --samples with a cloud storage (S3) path

  bug
  bactopia/bactopia#679 · Filter by author rwilliams opened on Sep 4, 2026

• [bug]mob_recon fails with TypeError: NDFrame.to_csv() got an unexpected keyword argument 'line_terminator'

  bug
  bactopia/bactopia#678 · Filter by author kruem-ar opened on Aug 24, 2026

• [bug] Merlin failing when 0 contigs assembled

  bug
  bactopia/bactopia#677 · Filter by author coxrs opened on Aug 18, 2026
  1

• [bactopia-tool] Add ConFindr for bacterial isolate contamination screening

  add-bactopia-tool
  bactopia/bactopia#657 · Filter by author JaneZheng-0406 opened on Apr 27, 2026
  6

• Processes exceeding running time limit

  bug
  bactopia/bactopia#643 · Filter by author AntonS-bio opened on Jan 14, 2026

• R1 R2 error correction

  bactopia/bactopia#641 · Filter by author fconstancias opened on Dec 9, 2025

• Incompatible Python versions

  bug
  bactopia/bactopia#640 · Filter by author AntonS-bio opened on Dec 2, 2025
  2

• [question] Preassembled genome with reads

  question
  bactopia/bactopia#635 · Filter by author SchwarzMarek opened on Oct 27, 2025
  2

• [question] Using Bactopia on HPC with SLURM workload management

  question
  bactopia/bactopia#634 · Filter by author michaelgruenstaeudl opened on Oct 22, 2025
  4

• Using files contained in subdirectories

  enhancementv4.1
  bactopia/bactopia#633 · Filter by author AntonS-bio opened on Oct 21, 2025
  2

• [ bactopia tool ] - CCNE and/or PCNE

  add-bactopia-toolv4
  bactopia/bactopia#629 · Filter by author riccabolla opened on Aug 29, 2025
  4

• [feature] Bactopia Summary support for clean-yer-reads

  enhancementv4.1
  bactopia/bactopia#626 · Filter by author coxrs opened on Jul 25, 2025

• [bug] bactopia fails upon estimating genome size using kmc

  bugv4
  bactopia/bactopia#624 · Filter by author en-no opened on Jul 11, 2025

• [bug] SKESA OOM Failure Reporting

  bugv4
  bactopia/bactopia#617 · Filter by author wtporter opened on Jun 10, 2025
  5

• [question] Using mashtree with bactopia results for local files AND taxid sample

  questionv4
  bactopia/bactopia#616 · Filter by author aperreault opened on Jun 10, 2025
  2

• [feature] Support for PacBio reads

  enhancementv4
  bactopia/bactopia#615 · Filter by author vigzy77 opened on May 2, 2025

• [question] Snippy failing when aligning to subset of reference

  questionv4
  bactopia/bactopia#613 · Filter by author nmmahmed opened on Apr 15, 2025

• Amrfinder plus summary

  questionv4
  bactopia/bactopia#612 · Filter by author andreaniml opened on Apr 14, 2025
  1

• [bug] Install of bactopia 3.2.0 not working on apple silicon due to wget not being available on it from anaconda

  bugv4
  bactopia/bactopia#611 · Filter by author kimleeng opened on Apr 11, 2025
  1

• [bug] Snippy output differs from docs

  bugv4
  bactopia/bactopia#610 · Filter by author ammaraziz opened on Apr 10, 2025

• [feature] Request for Addition to VFDB Full Database

  enhancementv4
  bactopia/bactopia#609 · Filter by author llk578496 opened on Apr 1, 2025

• [feature] Enhance AMRFinderPlus Module for Mutational Resistance and Organism-Specific Filtering

  enhancementv4.1
  bactopia/bactopia#604 · Filter by author dejenie21 opened on Mar 21, 2025
  4

• [feature] Handling of skesa's --allow_snps and --depth options

  enhancementv4
  bactopia/bactopia#602 · Filter by author iferres opened on Mar 12, 2025
  3