💾 📃 "Reads to report" for public health and clinical microbiology

A resistome profiler for Graphing Resistance Out Of meTagenomes

Bacterial analysis toolbox for full ESKAPE pathogen characterization and profiling the resistome, mobilome, virulome & phylogenomics using WGS

JAMIRA is a reproducible Workflow for Integrative Exploration of Genomic Features of prokariotes

A pipeline for Detecting Resistome Associated taXa

This repository contains tools and resources developed by Team Lahti during the "Resistance is Futile: A Codeathon to Combat Antimicrobial Resistance" (September 2024), hosted by NCBI and NIAID.

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

Predicts bacterial resistome

Mapping, snps calling, phylogeny

A Computational Pipeline for Ranking Resistome Risk of Metagenomic Samples

Zero-shot protein language model pipeline for mutational tolerance scoring of antibiotic resistance genes in ESKAPE pathogens

Graph-based pangenomic and synteny analysis of Helicobacter pylori (n=41 complete RefSeq genomes) using PPanGGOLiN, with reproducible workflows for annotation (Prokka), ANI quality control (FastANI), core-genome phylogeny (MAFFT + IQ-TREE 2), resistome profiling (AMRFinderPlus), and publication-grade visualizations.

A comprehensive pan-immunophagomic analysis of Pseudomonas aeruginosa, characterizing CRISPR-Cas arrays, prophage integrations, and innate bacterial defense repertoires across diverse clinical isolates.

Oral metagenomic analysis of antimicrobial resistance genes associated with periodontitis

A number of pipelines that are managed by Gnu Make for conducting various analyses on high-throughput NGS

A WGCNA pipeline systematically interrogating the Campylobacter resistome through topological network scaling to uncover co-expressed stress-response loci and significant module-trait biological correlations.