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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 109 16

  2. lathe lathe Public

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

    Python 69 18

  3. kraken2_classification kraken2_classification Public

    Snakemake workflow for metagenomic classification with Kraken2

    Python 66 16

  4. phanta phanta Public

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

    Python 60 9

  5. bhattlab_workflows bhattlab_workflows Public

    Computational workflows for metagenomics tasks, by the Bhatt lab

    Python 46 15

  6. StrainSifter StrainSifter Public

    A straightforward bioinformatic pipeline for detecting a bacterial strain in one or more metagenome(s).

    Python 19 3

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 60 MIT 9 2 1 Updated Oct 12, 2024
  • 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 Sep 20, 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
  • AWIGen2Microbiome Public

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

    bhattlab/AWIGen2Microbiome’s past year of commit activity
    R 3 MIT 1 2 0 Updated Jun 4, 2024
  • 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 Apr 5, 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 109 MIT 16 6 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 66 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 14 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
  • bhattlab/SouthAfrica’s past year of commit activity
    R 0 0 0 0 Updated Nov 20, 2021

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