salmonella

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

UPHL's Reference Free Pipeline

Various scripts for efficient processing of 10k Salmonella genomes

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

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

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

This Nextflow pipeline, gelidonyAMR, has been developed for analyzing Salmonella Infantis genomes, including genome assembly, antimicrobial resistance (AMR) profiling, MLST and cgMLST typing. It is designed for use in a Conda environment and is part of the my PhD project

RNA-Seq analysis pipeline for Salmonella using the READemption framework. This repository covers quality control, read mapping, transcript quantification, differential gene expression analysis, and result visualization, providing a reproducible workflow for bacterial transcriptomics from raw sequencing data to biological insights.

CGPS implementation of Genotyphi for assembled genomes.

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

Bioinformatics tool for Salmonella WGS analysis

A reproducible bioinformatics pipeline for processing, quality-checking, and analyzing bacterial Whole Genome Sequencing (WGS) data.

Dinh-Huy Nguyen - Specialized in Bacteria-mediated Cancer Immunotherapy

SEPI - Salmonella enterica poultry imports . Data analysis code for the study 'Genomic surveillance of Salmonella enterica Minnesota strains from poultry products imported into South Africa'

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

next-gen pangenome graphs for predictive genomics

Salmonella typhi; analysis pipeline for Illumina reads

Developed a deep learning model using CNNs to classify chicken fecal images, enabling early detection of diseases like Coccidiosis and Salmonella.