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@bokulich-lab Laboratory of Food Systems Biotechnology

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    25 repositories

    • mishmash

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•7•0•Updated Feb 28, 2025Feb 28, 2025

    • 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 AMRFinderPlus.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•1•1•Updated Feb 21, 2025Feb 21, 2025

    • q2-kmerizer

      Public
      QIIME 2 plugin for generating kmers from biological sequences
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Feb 21, 2025Feb 21, 2025

    • moshpit-docs

      Public
      MOSHPIT plugin suite documentation
      TeX
      •
      BSD 3-Clause "New" or "Revised" License
      •5•0•0•0•Updated Feb 19, 2025Feb 19, 2025

    • q2-annotate

      Public
      QIIME 2 plugin for functional annotation and taxonomic classification of shotgun metagenomes.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •14•3•18•4•Updated Feb 18, 2025Feb 18, 2025

    • q2-fastp

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•0•Updated Feb 13, 2025Feb 13, 2025

    • RESCRIPt

      Public
      REference Sequence annotation and CuRatIon Pipeline
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •26•96•17•2•Updated Feb 10, 2025Feb 10, 2025

    • q2-viromics

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •4•0•1•0•Updated Feb 4, 2025Feb 4, 2025

    • MOSHPIT

      Public
      Provides "mosh" cli command and "moshpit" proxy package.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Jan 18, 2025Jan 18, 2025

    • q2-fondue

      Public
      Functions for reproducibly Obtaining and Normalizing Data re-Used from Elsewhere
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •7•21•11•1•Updated Jan 18, 2025Jan 18, 2025

    • q2-assembly

      Public
      QIIME 2 plugin for (meta)genome assembly.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •13•4•8•0•Updated Jan 18, 2025Jan 18, 2025

    • q2-ms

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•13•10•Updated Jan 15, 2025Jan 15, 2025

    • q2-pinocchio

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•1•2•3•Updated Jan 15, 2025Jan 15, 2025

    • q2-virsorter2

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•0•0•0•Updated Jan 9, 2025Jan 9, 2025

    • utilities

      Public
      A collection of utilities used across repos.
      Shell
      •1•0•0•0•Updated Dec 20, 2024Dec 20, 2024

    • q2-rgi

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•2•3•3•Updated Dec 9, 2024Dec 9, 2024

    • nf-ducken

      Public
      Workflow to process amplicon meta-analysis data, from NCBI accession IDs to taxonomic diversity metrics.
      Nextflow
      •3•4•44•0•Updated Oct 24, 2024Oct 24, 2024

    • FermDB

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•0•0•Updated Sep 29, 2024Sep 29, 2024

    • Fermented-Food-Ontologies

      Public
      Substrate-based fermented food ontologies
      Python
      •
      Creative Commons Attribution 4.0 International
      •1•0•0•1•Updated Jul 12, 2024Jul 12, 2024

    • 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•2•0•Updated Jun 5, 2024Jun 5, 2024

    • 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

    • q2-exonerate

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jan 23, 2024Jan 23, 2024

    • q2-protein-pca

      Public
      QIIME2 plugin for PCA analysis of protein sequence phylogeny.
      pcaqiime2protein
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•3•9•0•Updated Jul 12, 2022Jul 12, 2022

    • q2-plugin-template

      Public template
      A skeleton for QIIME 2 plugins
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•3•0•0•Updated Jun 29, 2022Jun 29, 2022

    • q2-coordinates

      Public
      methods for geographic mapping of qiime2 artifact data or metadata
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •8•2•10•0•Updated Feb 4, 2022Feb 4, 2022