Collection of 1069 Escherichia coli virulence factors

Docker-based implementation of the Discover1.1 pipeline for bacterial characterization.

The files in this repository reproduce all the simulations and graphs in the paper, Fofana & Hurford 2022, Parasite-induced shifts in host movement may explain the transient coexistence of high- and low-pathogenic disease strains, J Evol Biol.

Sets of protein familes represented as profile HMMs annotated for antibiotic resistance and virulence function.

Docker-based implementation of the Discover1.1 pipeline for bacterial characterization.

Bacterial swiss-army-knife pipeline for NGS data

Determines the serotype and virulence in Escherichia coli isolates using NGS data (reads) through kmer alignment.