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@bactopia Bactopia

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    17 repositories

    • bactopia

      Public
      A flexible pipeline for complete analysis of bacterial genomes
      nextflowcondabiocondabacterial-genomesfastqs
      Nextflow
      •
      MIT License
      •79•498•104•1•Updated Dec 19, 2025Dec 19, 2025

    • nf-bactopia

      Public
      A Nextflow plugin for Bactopia
      Groovy
      •
      Apache License 2.0
      •0•1•0•0•Updated Nov 26, 2025Nov 26, 2025

    • bactopia-py

      Public
      A Python package for working with Bactopia
      Python
      •
      MIT License
      •2•12•0•1•Updated Oct 31, 2025Oct 31, 2025

    • bactopia-tests

      Public
      Contains data used by Bactopia for testing.
      Standard ML
      •
      MIT License
      •2•4•0•0•Updated Mar 10, 2025Mar 10, 2025

    • bactopia.github.io

      Public
      Bactopia Documentation
      Jinja
      •
      MIT License
      •12•3•0•2•Updated 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
      •651•0•0•0•Updated Oct 15, 2024Oct 15, 2024

    • bactopia-teton

      Public
      The taxonomic classification process used by Bactopia.
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 2, 2024Oct 2, 2024

    • bactopia-qc

      Public
      The methods used in Bactopia for read QC
      Shell
      •
      MIT License
      •0•0•0•0•Updated Sep 20, 2024Sep 20, 2024

    • bactopia-assembler

      Public
      The assembly process used by Bactopia.
      Shell
      •
      MIT License
      •0•3•0•0•Updated Mar 24, 2024Mar 24, 2024

    • bactopia-variants

      Public
      The SNP and InDel process used by Bactopia
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 15, 2024Mar 15, 2024

    • bactopia-sketcher

      Public
      Methods used by Bactopia for minmer sketching
      Shell
      •
      MIT License
      •0•0•0•0•Updated Oct 3, 2023Oct 3, 2023

    • bactopia-gather

      Public
      The methods used in Bactopia to gather all samples into one place
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 11, 2023Aug 11, 2023

    • bactopia-workshop

      Public
      A workshop on getting started with Bactopia
      MIT License
      •1•2•0•0•Updated May 10, 2023May 10, 2023

    • bactopia-wdl

      Public
      A WDL wrapper around Bactopia
      WDL
      •
      MIT License
      •0•0•0•0•Updated Jul 26, 2022Jul 26, 2022

    • bactopia-results

      Public
      A repository for example result files generated by Bactopia
      MIT License
      •0•0•0•0•Updated Mar 1, 2022Mar 1, 2022

    • bactopia-msystems-2020

      Public
      Scripts and data associated with Bactopia publication in mSystems
      HTML
      •
      MIT License
      •0•0•0•0•Updated Nov 30, 2021Nov 30, 2021

    • bactopia-datasets

      Public archive
      A list of curated species-specific datasets.
      MIT License
      •0•1•0•0•Updated Apr 13, 2021Apr 13, 2021