Pinned Repositories
AWIGen2Microbiome
Repository for the AWI-Gen 2 microbiome project workflows, analysis, and results.
bhattlab_workflows
Computational workflows for metagenomics tasks, by the Bhatt lab
kraken2_classification
Snakemake workflow for metagenomic classification with Kraken2
lathe
A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
metagenomics_workflows
Workflows for metagenomic sequence data processing and analysis.
MGEfinder
A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
phanta
Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes
scg_tools
Useful utilities for using the SCG cluster.
SmORFinder
A command line tool to identify and annotate small proteins in microbial sequencing datasets.
StrainSifter
A straightforward bioinformatic pipeline for detecting a bacterial strain in one or more metagenome(s).
bhattlab's Repositories
bhattlab/MGEfinder
A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
bhattlab/lathe
A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
bhattlab/kraken2_classification
Snakemake workflow for metagenomic classification with Kraken2
bhattlab/phanta
Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes
bhattlab/bhattlab_workflows
Computational workflows for metagenomics tasks, by the Bhatt lab
bhattlab/StrainSifter
A straightforward bioinformatic pipeline for detecting a bacterial strain in one or more metagenome(s).
bhattlab/SmORFinder
A command line tool to identify and annotate small proteins in microbial sequencing datasets.
bhattlab/metagenomics_workflows
Workflows for metagenomic sequence data processing and analysis.
bhattlab/scg_tools
Useful utilities for using the SCG cluster.
bhattlab/AWIGen2Microbiome
Repository for the AWI-Gen 2 microbiome project workflows, analysis, and results.
bhattlab/Benchmarking
Repository for 2021 sample stability benchmarking data analysis and figures
bhattlab/slurm
Cookiecutter for snakemake slurm profile
bhattlab/SupplementaryInformation
Supplementary information for some of our lab's publications.
bhattlab/pipelines
Data processing and analysis pipelines
bhattlab/SouthAfrica
bhattlab/absolute-abundance-16s
absolute abundance calculations from 16S rRNA qPCR or ddPCR
bhattlab/BacMetSearch
A command line tool to perform local DIAMOND searches against the BacMet database.
bhattlab/bhattlab_workflows_nf
Computational workflows for metagenomics tasks, packaged with Nextflow and Singularity.
bhattlab/buckley
bhattlab/DeepKingNet
A command line tool to classify nucleotide sequences as prokaryotic or eukaryotic.
bhattlab/durrant
bhattlab/hmmetariboseq
HMM for Metaribosq
bhattlab/islandest
A command line tool to identify and annotate tRNA-targeting genomic islands
bhattlab/MGEfinder-singularity
A singularity image for the MGEfinder software
bhattlab/plate-qc
A pipeline for assessing cross-contamination in high throughput metagenomic sequencing, and guidelines for upstream preventative measures.
bhattlab/processing16S_dada2
bhattlab/sweng
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.
bhattlab/wits_workshop