Issues

Issues

• [bug] QC Module error in test

  bactopia/bactopia#684 · opened on Oct 20, 2026
  2

• [question] Question about Lighter being used twice

  bactopia/bactopia#683 · opened on Sep 25, 2026

• [feature]

  bactopia/bactopia#681 · opened on Sep 22, 2026

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

  bactopia/bactopia#679 · opened on Sep 4, 2026

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

  bactopia/bactopia#678 · opened on Aug 24, 2026

• [bug] Merlin failing when 0 contigs assembled

  bactopia/bactopia#677 · opened on Aug 18, 2026
  1

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

  bactopia/bactopia#657 · opened on Apr 27, 2026
  6

• Processes exceeding running time limit

  bactopia/bactopia#643 · opened on Jan 14, 2026

• R1 R2 error correction

  bactopia/bactopia#641 · opened on Dec 9, 2025

• Incompatible Python versions

  bactopia/bactopia#640 · opened on Dec 2, 2025
  2

• [question] Preassembled genome with reads

  bactopia/bactopia#635 · opened on Oct 27, 2025
  2

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

  bactopia/bactopia#634 · opened on Oct 22, 2025
  4

• Using files contained in subdirectories

  bactopia/bactopia#633 · opened on Oct 21, 2025
  2

• [ bactopia tool ] - CCNE and/or PCNE

  bactopia/bactopia#629 · opened on Aug 29, 2025
  4

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

  bactopia/bactopia#626 · opened on Jul 25, 2025

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

  bactopia/bactopia#624 · opened on Jul 11, 2025

• [bug] SKESA OOM Failure Reporting

  bactopia/bactopia#617 · opened on Jun 10, 2025
  5

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

  bactopia/bactopia#616 · opened on Jun 10, 2025
  2

• [feature] Support for PacBio reads

  bactopia/bactopia#615 · opened on May 2, 2025

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

  bactopia/bactopia#613 · opened on Apr 15, 2025

• Amrfinder plus summary

  bactopia/bactopia#612 · 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

  bactopia/bactopia#611 · opened on Apr 11, 2025
  1

• [bug] Snippy output differs from docs

  bactopia/bactopia#610 · opened on Apr 10, 2025

• [feature] Request for Addition to VFDB Full Database

  bactopia/bactopia#609 · opened on Apr 1, 2025

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

  bactopia/bactopia#604 · opened on Mar 21, 2025
  4