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    • utilities

      Public
      A collection of utilities used across repos.
      Python
      1000Updated Apr 8, 2026Apr 8, 2026
    • q2-deseq2

      Public
      Python
      GNU Lesser General Public License v3.0
      1001Updated Apr 7, 2026Apr 7, 2026
    • QIIME 2 plugin for functional annotation and taxonomic classification of shotgun metagenomes.
      Python
      BSD 3-Clause "New" or "Revised" License
      204235Updated Apr 7, 2026Apr 7, 2026
    • q2-amrfinderplus: QIIME 2 plugin to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences with AMRFi…
      Python
      BSD 3-Clause "New" or "Revised" License
      3133Updated Apr 1, 2026Apr 1, 2026
    • MOSHPIT plugin suite documentation
      Makefile
      BSD 3-Clause "New" or "Revised" License
      8011Updated Apr 1, 2026Apr 1, 2026
    • QIIME 2 plugin for (meta)genome assembly.
      Python
      BSD 3-Clause "New" or "Revised" License
      142102Updated Mar 25, 2026Mar 25, 2026
    • QIIME 2 plugin for read mapping and analysis with Subread.
      Python
      GNU General Public License v3.0
      0000Updated Mar 18, 2026Mar 18, 2026
    • mishmash

      Public
      Python
      BSD 3-Clause "New" or "Revised" License
      3290Updated Mar 13, 2026Mar 13, 2026
    • q2-rgi

      Public
      This is a QIIME2 plugin that annotates sequence data with antimicrobial resistance gene information from CARD.
      Python
      BSD 3-Clause "New" or "Revised" License
      3352Updated Feb 26, 2026Feb 26, 2026
    • QIIME 2 plugin for submission of metadata and raw sequence reads to ENA.
      Python
      BSD 3-Clause "New" or "Revised" License
      1011Updated Feb 26, 2026Feb 26, 2026
    • QIIME 2 plugin for sequence alignment using minimap2.
      Python
      BSD 3-Clause "New" or "Revised" License
      3311Updated Feb 20, 2026Feb 20, 2026
    • QIIME2 plugin for quality control analysis of long-read sequences.
      Python
      BSD 3-Clause "New" or "Revised" License
      1200Updated Feb 20, 2026Feb 20, 2026
    • q2-skani

      Public
      QIIME 2 plugin for ANI analysis using skani.
      Python
      BSD 3-Clause "New" or "Revised" License
      1000Updated Feb 20, 2026Feb 20, 2026
    • q2-fondue

      Public
      Functions for reproducibly Obtaining and Normalizing Data re-Used from Elsewhere
      Python
      BSD 3-Clause "New" or "Revised" License
      824130Updated Feb 20, 2026Feb 20, 2026
    • Python
      BSD 3-Clause "New" or "Revised" License
      3010Updated Feb 20, 2026Feb 20, 2026
    • q2-gunc

      Public
      QIIME 2 plugin for analysis of genomes using GUNC.
      HTML
      BSD 3-Clause "New" or "Revised" License
      1000Updated Feb 20, 2026Feb 20, 2026
    • q2-fastp

      Public
      Python
      BSD 3-Clause "New" or "Revised" License
      1200Updated Feb 20, 2026Feb 20, 2026
    • q2-checkm

      Public
      QIIME 2 plugin for assessing the quality of (meta)genomes using CheckM.
      Python
      BSD 3-Clause "New" or "Revised" License
      3000Updated Feb 20, 2026Feb 20, 2026
    • RESCRIPt

      Public
      REference Sequence annotation and CuRatIon Pipeline
      Python
      BSD 3-Clause "New" or "Revised" License
      2598150Updated Feb 19, 2026Feb 19, 2026
    • Nextflow
      BSD 3-Clause "New" or "Revised" License
      1320Updated Feb 10, 2026Feb 10, 2026
    • Python
      BSD 3-Clause "New" or "Revised" License
      4022Updated Feb 6, 2026Feb 6, 2026
    • QIIME 2 plugin for generating kmers from biological sequences
      Python
      BSD 3-Clause "New" or "Revised" License
      4111Updated Jan 27, 2026Jan 27, 2026
    • MOSHPIT

      Public
      Provides "mosh" cli command and "moshpit" proxy package.
      Python
      BSD 3-Clause "New" or "Revised" License
      1001Updated Jan 27, 2026Jan 27, 2026
    • nf-ducken

      Public
      Workflow to process amplicon meta-analysis data, from NCBI accession IDs to taxonomic diversity metrics.
      Nextflow
      BSD 3-Clause "New" or "Revised" License
      44440Updated Sep 24, 2025Sep 24, 2025
    • Substrate-based fermented food ontologies
      Python
      Creative Commons Attribution 4.0 International
      4005Updated Sep 4, 2025Sep 4, 2025
    • q2-ms

      Public
      Python
      BSD 3-Clause "New" or "Revised" License
      10128Updated Aug 18, 2025Aug 18, 2025
    • A QIIME 2 plugin to annotate fungal taxonomies with lifestyle traits and spore volume data.
      Python
      BSD 3-Clause "New" or "Revised" License
      2022Updated Apr 23, 2025Apr 23, 2025
    • FermDB

      Public
      Python
      BSD 3-Clause "New" or "Revised" License
      5302Updated Mar 24, 2025Mar 24, 2025
    • Python
      BSD 3-Clause "New" or "Revised" License
      0000Updated Mar 14, 2025Mar 14, 2025
    • q2-types-genomics

      Public archive
      QIIME 2 types for genomics plugins.
      Python
      BSD 3-Clause "New" or "Revised" License
      11650Updated May 21, 2024May 21, 2024
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