💾 📃 "Reads to report" for public health and clinical microbiology
A resistome profiler for Graphing Resistance Out Of meTagenomes
A pipeline for Detecting Resistome Associated taXa
JAMIRA is a reproducible Workflow for Integrative Exploration of Genomic Features of prokariotes
Mapping, snps calling, phylogeny
Predicts bacterial resistome
A number of pipelines that are managed by Gnu Make for conducting various analyses on high-throughput NGS
Bacterial analysis toolbox for full ESKAPEE pathogen characterisation and profiling the resistome, mobilome, virulome & phylogenomics using WGS
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.
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 Computational Pipeline for Ranking Resistome Risk of Metagenomic Samples
Repo for scripts/codes applied in my studies
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