escherichia-coli

EcoliTyper: A species-optimized computational pipeline for comprehensive genotyping and surveillance of Escherichia coli. Perfect for clinical microbiology, outbreak investigations, and genomic research.

StxTyper uses a standardized algorithm to accurately type both known and unknown Shiga toxin operons from assembled genomic sequence.

Kinetic modeling of glucose and acetate metabolisms in E. coli

The AMRnet dashboard aims to make high-quality, robust and reliable genome-derived AMR surveillance data accessible to a wide audience

Data and tools necessary to construct iJL1678b-ME, a genome-scale model of E. coli K-12 MG1655 metabolism and expression

Escherichia coli Transcriptome Assembly from a Compendium of RNA-seq Data Sets

Code for ML-based detection of unstable antibiotic heteroresistance in E. coli genomic data

Machine learning pipeline for genome-scale metabolic engineering and intervention ranking in E. coli using COBRApy and FBA.

Exploring correlations in an isobaric labeling mass spectrometry-based proteomic data set

In silico PCR command line tool for typing Escherichia coli ST131

IRIDA plugin for ECTyper (E.coli in silico typing tool)

Nanopore amplicon multilocus sequence typing (MLST): Snakemake workflow with PubMLST scheme packs

Predicting the regulatory role of CRP transcription factor in Escherichia coli

13C metabolic flux analysis of the extracellular GL-GNT by-pass of E. coli

A command-line tool for predicting K-antigen type classifications in Escherichia coli.

Code and input files to reproduce the analyses in the manuscript "The natural diversity of E. coli capsules".

The KlebGen project is a genomics surveillance initiative focused on Klebsiella Pneumoniae and E. Coli strains isolated from neonates across Africa. This repository contains all the scripts used to analyze the strains from the Cameroonian subset of the project.

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 project is a model-first, constraint-aware approach to engineering E. coli Nissle 1917 (EcN) as a gut sentinel: sensing context, responding with targeted antimicrobials, and remaining governable through built-in containment.

Decipher polymorphism in E. coli strains with coevolutionary models