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@bokulich-lab Laboratory of Food Systems Biotechnology

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    34 repositories

    • utilities

      Public
      A collection of utilities used across repos.
      Python
      •1•0•0•0•Updated Apr 8, 2026Apr 8, 2026

    • q2-deseq2

      Public
      Python
      •
      GNU Lesser General Public License v3.0
      •1•0•0•1•Updated Apr 7, 2026Apr 7, 2026

    • q2-annotate

      Public
      QIIME 2 plugin for functional annotation and taxonomic classification of shotgun metagenomes.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •20•4•23•5•Updated Apr 7, 2026Apr 7, 2026

    • q2-amrfinderplus

      Public
      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
      •3•1•3•3•Updated Apr 1, 2026Apr 1, 2026

    • moshpit-docs

      Public
      MOSHPIT plugin suite documentation
      Makefile
      •
      BSD 3-Clause "New" or "Revised" License
      •8•0•1•1•Updated Apr 1, 2026Apr 1, 2026

    • q2-assembly

      Public
      QIIME 2 plugin for (meta)genome assembly.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •14•2•10•2•Updated Mar 25, 2026Mar 25, 2026

    • q2-subread

      Public
      QIIME 2 plugin for read mapping and analysis with Subread.
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Mar 18, 2026Mar 18, 2026

    • mishmash

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•2•9•0•Updated Mar 13, 2026Mar 13, 2026

    • q2-rgi

      Public
      This is a QIIME2 plugin that annotates sequence data with antimicrobial resistance gene information from CARD.
      metagenomicsamrqiime2
      metagenomicsamrqiime2
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•3•5•2•Updated Feb 26, 2026Feb 26, 2026

    • q2-ena-uploader

      Public
      QIIME 2 plugin for submission of metadata and raw sequence reads to ENA.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•1•1•Updated Feb 26, 2026Feb 26, 2026

    • q2-minimap2

      Public
      QIIME 2 plugin for sequence alignment using minimap2.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•3•1•1•Updated Feb 20, 2026Feb 20, 2026

    • q2-long-reads-qc

      Public
      QIIME2 plugin for quality control analysis of long-read sequences.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•0•0•Updated Feb 20, 2026Feb 20, 2026

    • q2-skani

      Public
      QIIME 2 plugin for ANI analysis using skani.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated 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
      •8•24•13•0•Updated Feb 20, 2026Feb 20, 2026

    • q2-virsorter2

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•0•1•0•Updated 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
      •1•0•0•0•Updated Feb 20, 2026Feb 20, 2026

    • q2-fastp

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•0•0•Updated 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
      •3•0•0•0•Updated Feb 20, 2026Feb 20, 2026

    • RESCRIPt

      Public
      REference Sequence annotation and CuRatIon Pipeline
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •25•98•15•0•Updated Feb 19, 2026Feb 19, 2026

    • nf-moshpit

      Public
      Nextflow
      •
      BSD 3-Clause "New" or "Revised" License
      •1•3•2•0•Updated Feb 10, 2026Feb 10, 2026

    • q2-viromics

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •4•0•2•2•Updated Feb 6, 2026Feb 6, 2026

    • q2-kmerizer

      Public
      QIIME 2 plugin for generating kmers from biological sequences
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •4•1•1•1•Updated Jan 27, 2026Jan 27, 2026

    • MOSHPIT

      Public
      Provides "mosh" cli command and "moshpit" proxy package.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•1•Updated 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
      •4•4•44•0•Updated Sep 24, 2025Sep 24, 2025

    • Fermented-Food-Ontologies

      Public
      Substrate-based fermented food ontologies
      Python
      •
      Creative Commons Attribution 4.0 International
      •4•0•0•5•Updated Sep 4, 2025Sep 4, 2025

    • q2-ms

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•12•8•Updated Aug 18, 2025Aug 18, 2025

    • q2-fungal-traits

      Public
      A QIIME 2 plugin to annotate fungal taxonomies with lifestyle traits and spore volume data.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•2•2•Updated Apr 23, 2025Apr 23, 2025

    • FermDB

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •5•3•0•2•Updated Mar 24, 2025Mar 24, 2025

    • q2-sort-me-rna

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Mar 14, 2025Mar 14, 2025

    • q2-types-genomics

      Public archive
      QIIME 2 types for genomics plugins.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •11•6•5•0•Updated May 21, 2024May 21, 2024
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