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    30 repositories

    • phanta

      Public
      Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes
      Python
      •
      MIT License
      •10•68•1•0•Updated Dec 1, 2025Dec 1, 2025

    • bhattlab_workflows_nf

      Public
      Computational workflows for metagenomics tasks, packaged with Nextflow and Singularity.
      Nextflow
      •
      MIT License
      •1•1•0•0•Updated Nov 4, 2025Nov 4, 2025

    • long_read_benchmark

      Public
      Analysis code and results for the long read benchmark project
      R
      •
      MIT License
      •0•0•0•0•Updated Aug 26, 2025Aug 26, 2025

    • AWIGen2Microbiome

      Public
      Repository for the AWI-Gen 2 microbiome project workflows, analysis, and results.
      R
      •
      MIT License
      •2•4•1•0•Updated Feb 6, 2025Feb 6, 2025

    • absolute-abundance-16s

      Public
      absolute abundance calculations from 16S rRNA qPCR or ddPCR
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Jan 10, 2025Jan 10, 2025

    • Benchmarking

      Public
      Repository for 2021 sample stability benchmarking data analysis and figures
      HTML
      •0•2•0•0•Updated Jul 25, 2024Jul 25, 2024

    • GenomeSearch

      Public
      Quickly search for closely related microbial genomes using a marker-gene based approach.
      Python
      •0•0•2•0•Updated May 17, 2024May 17, 2024

    • MGEfinder

      Public
      A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
      Python
      •
      MIT License
      •18•125•11•2•Updated Oct 30, 2023Oct 30, 2023

    • kraken2_classification

      Public
      Snakemake workflow for metagenomic classification with Kraken2
      Python
      •17•66•4•0•Updated Jun 7, 2023Jun 7, 2023

    • SmORFinder

      Public
      A command line tool to identify and annotate small proteins in microbial sequencing datasets.
      Python
      •
      MIT License
      •4•25•2•1•Updated Mar 25, 2023Mar 25, 2023

    • bhattlab_workflows

      Public
      Computational workflows for metagenomics tasks, by the Bhatt lab
      Python
      •16•47•4•0•Updated Feb 6, 2023Feb 6, 2023

    • SouthAfrica

      Public
      R
      •0•2•0•0•Updated Nov 20, 2021Nov 20, 2021

    • lathe

      Public
      A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
      Python
      •
      MIT License
      •18•69•18•1•Updated Aug 10, 2021Aug 10, 2021

    • sweng

      Public
      sweng contains general software related notes, tools, documents etc. It also outlines various routine procedures and scripts that can be used by all team members.
      0•0•0•0•Updated Oct 20, 2020Oct 20, 2020

    • SupplementaryInformation

      Public
      Supplementary information for some of our lab's publications.
      0•1•0•0•Updated Oct 14, 2020Oct 14, 2020

    • DeepKingNet

      Public
      A command line tool to classify nucleotide sequences as prokaryotic or eukaryotic.
      Python
      •
      MIT License
      •1•0•0•0•Updated Oct 12, 2020Oct 12, 2020

    • BacMetSearch

      Public
      A command line tool to perform local DIAMOND searches against the BacMet database.
      Python
      •1•0•2•0•Updated Aug 27, 2020Aug 27, 2020

    • metagenomics_workflows

      Public
      Workflows for metagenomic sequence data processing and analysis.
      Python
      •11•7•0•0•Updated Aug 21, 2020Aug 21, 2020

    • MGEfinder-singularity

      Public
      A singularity image for the MGEfinder software
      0•0•0•0•Updated Apr 10, 2020Apr 10, 2020

    • islandest

      Public
      A command line tool to identify and annotate tRNA-targeting genomic islands
      Python
      •0•0•0•0•Updated Feb 4, 2020Feb 4, 2020

    • scg_tools

      Public
      Useful utilities for using the SCG cluster.
      Shell
      •3•5•2•0•Updated Jun 3, 2019Jun 3, 2019

    • processing16S_dada2

      Public
      R
      •1•0•0•0•Updated Jun 2, 2019Jun 2, 2019

    • wits_workshop

      Public archive
      Nextflow
      •0•0•0•0•Updated Jan 16, 2019Jan 16, 2019

    • slurm

      Public
      Cookiecutter for snakemake slurm profile
      Python
      •
      MIT License
      •52•2•0•0•Updated Sep 12, 2018Sep 12, 2018

    • StrainSifter

      Public
      A straightforward bioinformatic pipeline for detecting a bacterial strain in one or more metagenome(s).
      Python
      •3•19•1•0•Updated Jul 10, 2018Jul 10, 2018

    • plate-qc

      Public
      A pipeline for assessing cross-contamination in high throughput metagenomic sequencing, and guidelines for upstream preventative measures.
      Python
      •0•0•0•0•Updated Jun 18, 2018Jun 18, 2018

    • pipelines

      Public
      Data processing and analysis pipelines
      Python
      •1•0•0•0•Updated Mar 9, 2018Mar 9, 2018

    • hmmetariboseq

      Public
      HMM for Metaribosq
      Shell
      •1•0•0•1•Updated Oct 17, 2017Oct 17, 2017

    • durrant

      Public
      Python
      •0•0•0•0•Updated Dec 16, 2016Dec 16, 2016

    • buckley

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Dec 16, 2016Dec 16, 2016