The Genomic Epidemiology Application Ontology describes the genomics, laboratory, clinical and epidemiological contextual information required to support data sharing and integration for foodborne infectious disease surveillance and outbreak investigations.
☆24Feb 16, 2026Updated 2 weeks ago
Alternatives and similar repositories for genepio
Users that are interested in genepio are comparing it to the libraries listed below
Sorting:
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆29Jul 18, 2025Updated 7 months ago
- Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.☆13Dec 24, 2025Updated 2 months ago
- A simple pipeline for bacterial assembly and quality control☆16Feb 26, 2026Updated last week
- Dryad is a Nextflow pipeline for examining prokaryote relatedness. Dryad can perform a reference free analysis and/or SNP analysis.☆18Nov 20, 2025Updated 3 months ago
- A taxonomic classifier of plasmids☆28Jul 7, 2021Updated 4 years ago
- Experiments with using BIGSI data structure for metagenomic and QC applications☆19Aug 12, 2024Updated last year
- SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity☆13Aug 14, 2023Updated 2 years ago
- LYVE-SET, a method of using hqSNPs to create a phylogeny, especially for outbreak investigations☆27Aug 26, 2024Updated last year
- Predict MLST directly from uncorrected long reads☆27Oct 31, 2025Updated 4 months ago
- ☆21Jan 23, 2026Updated last month
- CFSAN Shigella Typing Pipeline☆15Jul 6, 2023Updated 2 years ago
- Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens☆37Jan 22, 2026Updated last month
- VIGOR4☆21Aug 15, 2025Updated 6 months ago
- Import script needed to build FluPRINT database from source☆11May 23, 2019Updated 6 years ago
- Ultrafast sequence typing and gene detection from NGS raw reads☆20Apr 15, 2021Updated 4 years ago
- In silico prediction of E. coli serotype, pathotype and shiga toxin subtyping☆65Jun 5, 2025Updated 9 months ago
- An open-source pathogen sequence database dedicated to equitable sharing, transparent governance, & empowering global public health.☆50Updated this week
- Genomic neighbor typing of bacterial pathogens using MinHash☆42Jan 10, 2023Updated 3 years ago
- rapid serotyping of Vibrio parahaemolyticus from whole genome sequencing data using serogroup-specific genes☆10Sep 2, 2021Updated 4 years ago
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories☆38Feb 20, 2026Updated last week
- serious constellations of reoccurring phylogenetically-independent origin☆39Feb 13, 2026Updated 2 weeks ago
- Bacterial surveillance pipeline.☆27Dec 30, 2025Updated 2 months ago
- Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies☆12Jun 30, 2023Updated 2 years ago
- Static website for the PH4AGE alliance☆13Oct 27, 2023Updated 2 years ago
- ☆10Apr 16, 2025Updated 10 months ago
- interactive barplot for amplicon sequencing☆13Dec 5, 2024Updated last year
- Posterior Analysis of Coalescent Trees☆14Aug 6, 2015Updated 10 years ago
- Intra-species bacterial contamination detection☆25Feb 5, 2026Updated last month
- UPHL's Reference Free Pipeline☆27Updated this week
- Freelance bioinformaticians directory☆10Feb 10, 2023Updated 3 years ago
- Workflow for viral analysis guided by reference☆17Feb 19, 2026Updated 2 weeks ago
- TreeKnit is a package that infers Ancestral Reassortment Graphs for segmented genomes (typically, human influenza).☆14Feb 18, 2025Updated last year
- Repository for Apollo-SV ontology. Versioning Apollo-SV independently of the software was made easiest by having it as a separate reposi…☆11Dec 24, 2024Updated last year
- whole genome MLST analysis☆51Feb 26, 2026Updated last week
- 🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission☆28Feb 19, 2026Updated 2 weeks ago
- A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.☆35Dec 2, 2024Updated last year
- Indexes genomes using SNVs, MLST, or kmers for rapid querying, clustering, and visualization.☆12Feb 2, 2023Updated 3 years ago
- 2025 RAD microbes boot camp☆15Apr 30, 2025Updated 10 months ago
- Ampseer examines reads in fastq format and identifies which multiplex PCR primer set was used to generate the SARS-CoV-2 sequencing libra…☆15Feb 27, 2024Updated 2 years ago