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    • bactopia

      Public
      A flexible pipeline for complete analysis of bacterial genomes
      Nextflow
      MIT License
      795011061Updated Mar 10, 2026Mar 10, 2026
    • nf-bactopia

      Public
      A Nextflow plugin for Bactopia
      Groovy
      Apache License 2.0
      0100Updated Mar 9, 2026Mar 9, 2026
    • bactopia-py

      Public
      A Python package for working with Bactopia
      Python
      MIT License
      21201Updated Mar 9, 2026Mar 9, 2026
    • bactopia-tests

      Public
      Contains data used by Bactopia for testing.
      Standard ML
      MIT License
      2400Updated Mar 10, 2025Mar 10, 2025
    • bactopia.github.io

      Public
      Bactopia Documentation
      Jinja
      MIT License
      12302Updated Oct 21, 2024Oct 21, 2024
    • bactopia-mqc

      Public
      Aggregate results from bioinformatics analyses across many samples into a single report.
      JavaScript
      GNU General Public License v3.0
      655000Updated Oct 15, 2024Oct 15, 2024
    • bactopia-teton

      Public
      The taxonomic classification process used by Bactopia.
      Python
      MIT License
      0000Updated Oct 2, 2024Oct 2, 2024
    • bactopia-qc

      Public
      The methods used in Bactopia for read QC
      Shell
      MIT License
      0000Updated Sep 20, 2024Sep 20, 2024
    • bactopia-assembler

      Public
      The assembly process used by Bactopia.
      Shell
      MIT License
      0300Updated Mar 24, 2024Mar 24, 2024
    • bactopia-variants

      Public
      The SNP and InDel process used by Bactopia
      Python
      MIT License
      0000Updated Mar 15, 2024Mar 15, 2024
    • Methods used by Bactopia for minmer sketching
      Shell
      MIT License
      0000Updated Oct 3, 2023Oct 3, 2023
    • The methods used in Bactopia to gather all samples into one place
      Python
      MIT License
      0000Updated Aug 11, 2023Aug 11, 2023
    • A workshop on getting started with Bactopia
      MIT License
      1200Updated May 10, 2023May 10, 2023
    • A WDL wrapper around Bactopia
      WDL
      MIT License
      0000Updated Jul 26, 2022Jul 26, 2022
    • A repository for example result files generated by Bactopia
      MIT License
      0000Updated Mar 1, 2022Mar 1, 2022
    • Scripts and data associated with Bactopia publication in mSystems
      HTML
      MIT License
      0000Updated Nov 30, 2021Nov 30, 2021
    • bactopia-datasets

      Public archive
      A list of curated species-specific datasets.
      MIT License
      0100Updated Apr 13, 2021Apr 13, 2021