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bhattlab

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  1. MGEfinder MGEfinder Public

    A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.

    Python 115 17

  2. lathe lathe Public

    A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing

    Python 70 18

  3. kraken2_classification kraken2_classification Public

    Snakemake workflow for metagenomic classification with Kraken2

    Python 65 16

  4. phanta phanta Public

    Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes

    Python 63 10

  5. bhattlab_workflows bhattlab_workflows Public

    Computational workflows for metagenomics tasks, by the Bhatt lab

    Python 46 15

  6. SmORFinder SmORFinder Public

    A command line tool to identify and annotate small proteins in microbial sequencing datasets.

    Python 20 4

Repositories

Showing 10 of 28 repositories
  • phanta Public

    Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes

    bhattlab/phanta’s past year of commit activity
    Python 63 MIT 10 1 0 Updated Mar 8, 2025
  • AWIGen2Microbiome Public

    Repository for the AWI-Gen 2 microbiome project workflows, analysis, and results.

    bhattlab/AWIGen2Microbiome’s past year of commit activity
    R 4 MIT 1 0 0 Updated Feb 6, 2025
  • absolute-abundance-16s Public

    absolute abundance calculations from 16S rRNA qPCR or ddPCR

    bhattlab/absolute-abundance-16s’s past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated Jan 10, 2025
  • bhattlab_workflows_nf Public

    Computational workflows for metagenomics tasks, packaged with Nextflow and Singularity.

    bhattlab/bhattlab_workflows_nf’s past year of commit activity
    Nextflow 0 MIT 0 0 0 Updated Oct 31, 2024
  • Benchmarking Public

    Repository for 2021 sample stability benchmarking data analysis and figures

    bhattlab/Benchmarking’s past year of commit activity
    HTML 2 0 0 0 Updated Jul 25, 2024
  • MGEfinder Public

    A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.

    bhattlab/MGEfinder’s past year of commit activity
    Python 115 MIT 17 8 2 Updated Oct 30, 2023
  • kraken2_classification Public

    Snakemake workflow for metagenomic classification with Kraken2

    bhattlab/kraken2_classification’s past year of commit activity
    Python 65 16 4 0 Updated Jun 7, 2023
  • SmORFinder Public

    A command line tool to identify and annotate small proteins in microbial sequencing datasets.

    bhattlab/SmORFinder’s past year of commit activity
    Python 20 MIT 4 2 1 Updated Mar 25, 2023
  • bhattlab_workflows Public

    Computational workflows for metagenomics tasks, by the Bhatt lab

    bhattlab/bhattlab_workflows’s past year of commit activity
    Python 46 15 4 0 Updated Feb 6, 2023
  • SouthAfrica Public
    bhattlab/SouthAfrica’s past year of commit activity
    R 2 0 0 0 Updated Nov 20, 2021

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