SISTR (Salmonella In Silico Typing Resource) command-line tool
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Apr 24, 2025 - Python
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serotyping
Here are 10 public repositories matching this topic...
UPHL's Reference Free Pipeline
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Mar 10, 2026 - Nextflow
EcoliTyper: A species-optimized computational pipeline for comprehensive genotyping and surveillance of Escherichia coli. Perfect for clinical microbiology, outbreak investigations, and genomic research.
bioinformatics computational-biology public-health epidemiology microbial-genomics mlst ecoli escherichia-coli cge serotyping genotyping outbreak-investigation pathogen-surveillance strain-typing clermont-typing
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Mar 7, 2026 - Python
In silico serotype prediction for Listeria monocytogenes
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Feb 23, 2026 - Python
E. coli K-antigen group 2 and group 3 typing database
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Mar 6, 2026 - R
IRIDA plugin for ECTyper (E.coli in silico typing tool)
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May 21, 2025 - Java
Pathogen whole genome sequence (WGS) data analysis pipeline
nanopore pathogen taxonomy assembly ngs amr mlst illumina plasmid serotyping virulome emm-typing capsular-typing
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Jan 30, 2026 - Nextflow
A command-line tool for predicting K-antigen type classifications in Escherichia coli.
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Mar 8, 2026 - Python
🧬 Analyze *Escherichia coli* strains efficiently with EcoliTyper, a unified tool for MLST, serotyping, and Clermont phylotyping in one workflow.
bioinformatics computational-biology public-health epidemiology microbial-genomics mlst ecoli escherichia-coli cge serotyping genotyping outbreak-investigation pathogen-surveillance strain-typing clermont-typing
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Mar 11, 2026 - Perl
IRIDA Plugin for SISTR Salmonella Typing Tool
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Mar 26, 2025 - Java
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