Skip to content
@bhattlab

bhattlab

Popular repositories

  1. MGEfinder MGEfinder Public

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

    Python 96 15

  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 65 16

  4. phanta phanta Public

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

    Python 55 7

  5. bhattlab_workflows bhattlab_workflows Public

    Computational workflows for metagenomics tasks, by the Bhatt lab

    Python 45 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 29 repositories
  • bhattlab_workflows_nf Public

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

    Nextflow 0 MIT 0 0 0 Updated Apr 22, 2024
  • absolute-abundance-16s Public

    absolute abundance calculations from 16S rRNA qPCR or ddPCR

    Jupyter Notebook 0 MIT 0 0 0 Updated Apr 5, 2024
  • AWIGen2Microbiome Public

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

    R 2 MIT 0 2 0 Updated Mar 25, 2024
  • Benchmarking Public

    Repository for 2021 sample stability benchmarking data analysis and figures

    HTML 2 0 0 0 Updated Mar 15, 2024
  • MGEfinder Public

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

    Python 96 MIT 15 3 2 Updated Oct 30, 2023
  • phanta Public

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

    Python 55 MIT 7 3 0 Updated Oct 23, 2023
  • kraken2_classification Public

    Snakemake workflow for metagenomic classification with Kraken2

    Python 65 16 2 0 Updated Jun 7, 2023
  • SmORFinder Public

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

    Python 12 MIT 2 1 1 Updated Mar 25, 2023
  • bhattlab_workflows Public

    Computational workflows for metagenomics tasks, by the Bhatt lab

    Python 45 15 4 0 Updated Feb 6, 2023
  • R 0 0 0 0 Updated Nov 20, 2021

People

This organization has no public members. You must be a member to see who’s a part of this organization.

Most used topics

Loading…