serotyping

The tool for in silico serotyping

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

UPHL's Reference Free Pipeline

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

In silico serotype prediction for Listeria monocytogenes

A species‑specific bioinformatics suite for rapid and accessible Pseudomonas aeruginosa genomic analysis

Nextflow pipeline for species-specific typing of bacteria

E. coli K-antigen group 2 and group 3 typing database

EnteroMark: A species-optimized computational pipeline for rapid, accessible Enterococcus faecium genotyping and surveillance .Complete VRE genomic analysis in minutes — not hours

Pathogen whole genome sequence (WGS) data analysis pipeline

Kaptive databases for the Klebsiella oxytoca Species Complex (and Klebsiella indica)

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

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

Kaptive databases for the Klebsiella pneumoniae Species Complex

Bacteria genomics data analysis pipeline from QC of fastq to Sequence typing. Including virulence, plasmid and AMR gene finding base on taxonomy and pylogenetic tree construction.

A template repo for managing Kaptive databases

IRIDA Plugin for SISTR Salmonella Typing Tool