bhattlab

MGEfinder

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

lathe

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

kraken2_classification

Snakemake workflow for metagenomic classification with Kraken2

phanta

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

bhattlab_workflows

Computational workflows for metagenomics tasks, by the Bhatt lab

StrainSifter

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

SmORFinder

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

metagenomics_workflows

Workflows for metagenomic sequence data processing and analysis.

scg_tools

Useful utilities for using the SCG cluster.

AWIGen2Microbiome

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

Benchmarking

Repository for 2021 sample stability benchmarking data analysis and figures

slurm

Cookiecutter for snakemake slurm profile

SupplementaryInformation

Supplementary information for some of our lab's publications.

pipelines

Data processing and analysis pipelines

SouthAfrica

absolute-abundance-16s

absolute abundance calculations from 16S rRNA qPCR or ddPCR

BacMetSearch

A command line tool to perform local DIAMOND searches against the BacMet database.

bhattlab_workflows_nf

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

buckley

DeepKingNet

A command line tool to classify nucleotide sequences as prokaryotic or eukaryotic.

durrant

hmmetariboseq

HMM for Metaribosq

islandest

A command line tool to identify and annotate tRNA-targeting genomic islands

MGEfinder-singularity

A singularity image for the MGEfinder software

plate-qc

A pipeline for assessing cross-contamination in high throughput metagenomic sequencing, and guidelines for upstream preventative measures.

processing16S_dada2

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.

wits_workshop