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absolute-abundance-16s

absolute abundance calculations from 16S rRNA qPCR or ddPCR

awigen2microbiome

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

bacmetsearch

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

benchmarking

Repository for 2021 sample stability benchmarking data analysis and figures

bhattlab_workflows

Computational workflows for metagenomics tasks, by the Bhatt lab

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

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.

mgefinder-singularity

A singularity image for the MGEfinder software

phanta

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

pipelines

Data processing and analysis pipelines

plate-qc

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

processing16s_dada2

scg_tools

Useful utilities for using the SCG cluster.

slurm

Cookiecutter for snakemake slurm profile

smorfinder

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

southafrica

strainsifter

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

supplementaryinformation

Supplementary information for some of our lab's publications.

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