Repositories list

• bactopia.github.io

  Public
  Bactopia Documentation

  MDX

  •

  MIT License

  •1212 forks in bactopia/bactopia.github.io•44 stars in bactopia/bactopia.github.io•00 issues in bactopia/bactopia.github.io•2020 pull requests in bactopia/bactopia.github.io•Updated Oct 29, 2026Oct 29, 2026

• nf-bactopia

  Public
  A Nextflow plugin for Bactopia

  Groovy

  •

  Apache License 2.0

  •11 fork in bactopia/nf-bactopia•33 stars in bactopia/nf-bactopia•00 issues in bactopia/nf-bactopia•00 pull requests in bactopia/nf-bactopia•Updated Oct 9, 2026Oct 9, 2026

• bactopia

  Public
  A flexible pipeline for complete analysis of bacterial genomes

  nextflowcondabioconda+ 2

  nextflowcondabiocondabacterial-genomesfastqs

  Nextflow

  •

  MIT License

  •8282 forks in bactopia/bactopia•525525 stars in bactopia/bactopia•6868 issues in bactopia/bactopia•22 pull requests in bactopia/bactopia•Updated Aug 5, 2026Aug 5, 2026

• bactopia-py

  Public
  A Python package for working with Bactopia

  Python

  •

  MIT License

  •33 forks in bactopia/bactopia-py•1212 stars in bactopia/bactopia-py•00 issues in bactopia/bactopia-py•11 pull request in bactopia/bactopia-py•Updated Aug 5, 2026Aug 5, 2026

• bactopia-tests

  Public
  Contains data used by Bactopia for testing.

  Standard ML

  •

  MIT License

  •22 forks in bactopia/bactopia-tests•44 stars in bactopia/bactopia-tests•00 issues in bactopia/bactopia-tests•11 pull request in bactopia/bactopia-tests•Updated Jul 28, 2026Jul 28, 2026

• bactopia-gather

  Public
  The methods used in Bactopia to gather all samples into one place

  Python

  •

  MIT License

  •00 forks in bactopia/bactopia-gather•00 stars in bactopia/bactopia-gather•00 issues in bactopia/bactopia-gather•00 pull requests in bactopia/bactopia-gather•Updated Jul 27, 2026Jul 27, 2026

• bactopia-teton

  Public
  The taxonomic classification process used by Bactopia.

  Python

  •

  MIT License

  •00 forks in bactopia/bactopia-teton•00 stars in bactopia/bactopia-teton•00 issues in bactopia/bactopia-teton•00 pull requests in bactopia/bactopia-teton•Updated May 6, 2026May 6, 2026

• bactopia-variants

  Public
  The SNP and InDel process used by Bactopia

  Python

  •

  MIT License

  •00 forks in bactopia/bactopia-variants•00 stars in bactopia/bactopia-variants•00 issues in bactopia/bactopia-variants•00 pull requests in bactopia/bactopia-variants•Updated Apr 4, 2026Apr 4, 2026

• bactopia-sketcher

  Public
  Methods used by Bactopia for minmer sketching

  Shell

  •

  MIT License

  •00 forks in bactopia/bactopia-sketcher•00 stars in bactopia/bactopia-sketcher•00 issues in bactopia/bactopia-sketcher•00 pull requests in bactopia/bactopia-sketcher•Updated Apr 3, 2026Apr 3, 2026

• bactopia-qc

  Public
  The methods used in Bactopia for read QC

  Shell

  •

  MIT License

  •00 forks in bactopia/bactopia-qc•00 stars in bactopia/bactopia-qc•00 issues in bactopia/bactopia-qc•00 pull requests in bactopia/bactopia-qc•Updated Apr 3, 2026Apr 3, 2026

• bactopia-assembler

  Public
  The assembly process used by Bactopia.

  Shell

  •

  MIT License

  •00 forks in bactopia/bactopia-assembler•33 stars in bactopia/bactopia-assembler•00 issues in bactopia/bactopia-assembler•00 pull requests in bactopia/bactopia-assembler•Updated Apr 3, 2026Apr 3, 2026

• bactopia-mqc

  Public
  Aggregate results from bioinformatics analyses across many samples into a single report.

  JavaScript

  •

  GNU General Public License v3.0

  •696696 forks in bactopia/bactopia-mqc•00 stars in bactopia/bactopia-mqc•00 issues in bactopia/bactopia-mqc•00 pull requests in bactopia/bactopia-mqc•Updated Oct 15, 2024Oct 15, 2024

• bactopia-workshop

  Public
  A workshop on getting started with Bactopia

  MIT License

  •22 forks in bactopia/bactopia-workshop•22 stars in bactopia/bactopia-workshop•00 issues in bactopia/bactopia-workshop•00 pull requests in bactopia/bactopia-workshop•Updated May 10, 2023May 10, 2023

• bactopia-wdl

  Public
  A WDL wrapper around Bactopia

  WDL

  •

  MIT License

  •00 forks in bactopia/bactopia-wdl•00 stars in bactopia/bactopia-wdl•00 issues in bactopia/bactopia-wdl•00 pull requests in bactopia/bactopia-wdl•Updated Jul 26, 2022Jul 26, 2022

• bactopia-outputs

  Public
  A repository for example result files generated by Bactopia

  MIT License

  •00 forks in bactopia/bactopia-outputs•00 stars in bactopia/bactopia-outputs•00 issues in bactopia/bactopia-outputs•00 pull requests in bactopia/bactopia-outputs•Updated Mar 1, 2022Mar 1, 2022

• bactopia-msystems-2020

  Public
  Scripts and data associated with Bactopia publication in mSystems

  HTML

  •

  MIT License

  •00 forks in bactopia/bactopia-msystems-2020•00 stars in bactopia/bactopia-msystems-2020•00 issues in bactopia/bactopia-msystems-2020•00 pull requests in bactopia/bactopia-msystems-2020•Updated Nov 30, 2021Nov 30, 2021

• bactopia-datasets

  Public archive
  A list of curated species-specific datasets.

  MIT License

  •00 forks in bactopia/bactopia-datasets•11 star in bactopia/bactopia-datasets•00 issues in bactopia/bactopia-datasets•00 pull requests in bactopia/bactopia-datasets•Updated Apr 13, 2021Apr 13, 2021