SISTR (Salmonella In Silico Typing Resource) command-line tool

Various scripts for efficient processing of 10k Salmonella genomes

Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.

Machine learning methods to predict the anti-microbial resistance of Salmonella.

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

CGPS implementation of Genotyphi for assembled genomes.

Fast assortment of Salmonella genomes into stable clusters using phylogenetic placement and kNN classifier

next-gen pangenome graphs for predictive genomics

Xenosiderophores produced by gut commensal fungi or present in the diet promote Salmonella enterica serovar Typhimurium growth and gut colonization

Salmonella typhi; analysis pipeline for Illumina reads

Bioinformatics tool for Salmonella WGS analysis

Detection, extraction, and cluster assignment of S. Infantis pESI