💾 📃 "Reads to report" for public health and clinical microbiology
Pathogen whole genome sequence (WGS) data analysis pipeline
This tool provides a modular WDL-Docker-Cromwell environment for rMAP, a bioinformatics pipeline for analyzing microbial genomic data, genome assembly & profiling of the resistome, mobilome & virulome, as well as pangenome & MLST typing, BLASTn & phylogenetic analysis. It includes all required tools, enabling reproducible & scalable analysis
A WDL-based workflow for profiling Klebsiella & E. coli genomes using Kleborate. Supports local execution with Cromwell both local & cloud deployment in Terra, enabling automated analysis of assemblies with docker & integration with Terra data tables for scalable genomic surveillance.
Bacterial analysis toolbox for full ESKAPEE pathogen characterisation and profiling the resistome, mobilome, virulome & phylogenomics using WGS
A config-driven R workflow for long-read shotgun metagenomics analysis
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