💾 📃 "Reads to report" for public health and clinical microbiology
A resistome profiler for Graphing Resistance Out Of meTagenomes
JAMIRA is a reproducible Workflow for Integrative Exploration of Genomic Features of prokariotes
A pipeline for Detecting Resistome Associated taXa
Mapping, snps calling, phylogeny
Predicts bacterial resistome
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 ready-to-use WDL-Docker-Cromwell environment for rMAP, a bioinformatics pipeline for analyzing microbial genomic data, Genome assembly & profiling Resistome, Mobilome & Virulome as well Pangenome & MLST typing, Blast & Phylogenetic analysis. It includes all required tools, enabling reproducible & scalable analysis of NGS data
A number of pipelines that are managed by Gnu Make for conducting various analyses on high-throughput NGS
Repo for scripts/codes applied in my studies
A Computational Pipeline for Ranking Resistome Risk of Metagenomic Samples
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