[{"src_path": "hub/tools/item-cgdist.md", "base_url": "https://globalmicrobialidentifier.org", "context_path": "hub/tools", "title": "cgDist: SNP and InDel distance calculator for *MLST", "date": "2025-07-26", "description": "Ultra-fast Rust implementation for calculating pairwise SNP and InDel level genetic distances from core and whole genome MLST (cg/wgMLST) profiles, designed for outbreak investigation and phylogenetic analysis in bacterial genomics. It adds a per-locus mutation-density screen that flags loci as recombination candidates for downstream confirmation, supports multiple hashing algorithms (CRC32, MD5, SHA256), and uses LZ4-compressed caching for memory-efficient processing of large datasets.", "terms": ["Software (Tool/Workflow)", "Microbial Typing", "Variant Detection", "Outbreak Detection/Investigation", "Pathogen-agnostic"], "thumbnail": null, "category": "Tools", "additional_metadata": {"kind": "resource", "link": "https://github.com/genpat-it/cgDist", "link_valid": true, "link_checked_at": "2026-09-25T10:36:06.912823"}, "page_number": 2, "directory": "hub", "items_per_page": 10}, {"src_path": "hub/tools/item-cgmlst-dists-py.md", "base_url": "https://globalmicrobialidentifier.org", "context_path": "hub/tools", "title": "cgmlst-dists-py: GPU-accelerated pairwise distance calculator for cgMLST", "date": "2024-04-22", "description": "High-performance Python reimplementation of cgmlst-dists for computing pairwise Hamming distances between cgMLST allelic profiles. It offers an optional Arrow-based loader that is three to four times faster at parsing large inputs and an optional CUDA path via numba for GPU acceleration, transparently falling back to the numpy CPU path with identical results when no usable device is present. Available on Bioconda and as a Docker image.", "terms": ["Software (Tool/Workflow)", "Microbial Typing", "Outbreak Detection/Investigation", "Pathogen-agnostic"], "thumbnail": null, "category": "Tools", "additional_metadata": {"kind": "resource", "link": "https://github.com/genpat-it/cgmlst-dists-py", "link_valid": true, "link_checked_at": "2026-09-25T10:36:06.912823"}, "page_number": 2, "directory": "hub", "items_per_page": 10}, {"src_path": "hub/tools/item-chewbbaca.md", "base_url": "https://globalmicrobialidentifier.org", "context_path": "hub/tools", "title": "chewBBACA: cg/wgMLST schema creation and allele calling suite", "date": "2017-08-04", "description": "Software suite for the creation and evaluation of core genome and whole genome MLST schemas and results, built on the BLAST Score Ratio based allele calling algorithm. It defines target loci from multiple genomes, performs allele calling to determine the allelic profiles of bacterial strains at the scale of thousands of genomes with modest computational resources, annotates schema loci, computes the core genome for a given dataset, and generates interactive reports for schema and allele calling evaluation in surveillance, outbreak detection and population study settings.", "terms": ["Software (Tool/Workflow)", "Microbial Typing", "Data Standardization/Harmonization", "Outbreak Detection/Investigation", "Pathogen-agnostic"], "thumbnail": null, "category": "Tools", "additional_metadata": {"kind": "resource", "link": "https://github.com/B-UMMI/chewBBACA", "link_valid": true, "link_checked_at": "2026-09-25T10:36:06.912823"}, "page_number": 3, "directory": "hub", "items_per_page": 10}, {"src_path": "hub/tools/item-chewcall.md", "base_url": "https://globalmicrobialidentifier.org", "context_path": "hub/tools", "title": "chewcall: high-performance cgMLST and wgMLST allele caller", "date": "2026-03-11", "description": "Rust allele caller for cgMLST and wgMLST schemas, compatible at the callable-DNA output level with chewBBACA. It replaces BLASTp with SIMD-accelerated exact Smith-Waterman protein alignment via parasail and ships a schema_audit binary that flags loci whose representative set is too sparse for the minimizer-overlap pre-filter. On eight BeONE benchmark datasets it runs 10.7 to 22.3 times faster than chewBBACA v3.5.4 while preserving 100 percent DNA-sequence agreement on bilaterally callable cells. Optional CUDA GPU mode is available.", "terms": ["Software (Tool/Workflow)", "Microbial Typing", "Outbreak Detection/Investigation", "Pathogen-agnostic"], "thumbnail": null, "category": "Tools", "additional_metadata": {"kind": "resource", "link": "https://github.com/genpat-it/chewcall", "link_valid": true, "link_checked_at": "2026-09-25T10:36:06.912823"}, "page_number": 1, "directory": "hub", "items_per_page": 10}, {"src_path": "hub/tools/item-cohesive.md", "base_url": "https://globalmicrobialidentifier.org", "context_path": "hub/tools", "title": "COHESIVE Information System (CIS)", "date": "2024-05-29", "description": "Docker-based deployment of the COHESIVE Information System, a web interface and database that integrates pathogen information from the medical and veterinary sectors to support One Health surveillance, outbreak investigation and risk assessment of zoonoses. Developed within the COHESIVE project, it is one of four IT tools designed to underpin integrated risk-analysis structures across EU member states, alongside the Decision Support Tool, the FoodChain-Lab web application and Shiny Rrisk.", "terms": ["Software (Platform)", "Systems Development", "One Health Surveillance", "Outbreak Detection/Investigation", "Pathogen-agnostic"], "thumbnail": null, "category": "Tools", "additional_metadata": {"kind": "resource", "link": "https://github.com/genpat-it/cohesive", "link_valid": true, "link_checked_at": "2026-09-25T10:36:06.912823"}, "page_number": 2, "directory": "hub", "items_per_page": 10}, {"src_path": "hub/tools/item-data-flo.md", "base_url": "https://globalmicrobialidentifier.org", "context_path": "hub/tools", "title": "Data-flo: open-source web application for data integration", "date": "2024-07-01", "description": "Open-source web application for data integration. It provides an easy-to-use visual interface to design reusable Workflows (data pipelines) that import, merge, clean and manipulate data in many different ways. Once a Workflow has been created, it can be run anytime, by anyone with access, to enable push-button data extraction and transformation, removing the bulk of the manual repetitive workflows that require multiple, sequential or tedious steps. It lets users rapidly prepare data for visualisation and reporting, share processed data between teams, consistently reproduce and validate data transformation procedures for updated or new datasets, and integrate data from multiple databases and sources. While used across many sectors, it contains a number of features tailored to manage bioinformatics-related datasets such as Newick and tree files.", "terms": ["Software (Platform)", "Data Curation", "Data Standardization/Harmonization", "Systems Development", "Pathogen-agnostic"], "thumbnail": null, "category": "Tools", "additional_metadata": {"kind": "resource", "link": "https://data-flo.io/", "link_valid": true, "link_checked_at": "2026-09-25T10:36:06.912823"}, "page_number": 2, "directory": "hub", "items_per_page": 10}, {"src_path": "hub/tools/item-dist2mst.md", "base_url": "https://globalmicrobialidentifier.org", "context_path": "hub/tools", "title": "dist2mst: Minimum Spanning Tree construction from distance matrices", "date": "2025-02-19", "description": "Tool for building Minimum Spanning Trees from symmetric distance matrices, with core numerical routines JIT-compiled and parallelised through Numba. It outputs standard Newick trees for downstream visualisation, groups nodes at zero Hamming distance, and provides hierarchical and targeted clustering with configurable path-distance thresholds, cluster size filtering and per-cluster Newick export. Available on Bioconda and as a Docker image.", "terms": ["Software (Tool/Workflow)", "Phylogenetic Tree Construction", "Outbreak Detection/Investigation", "Pathogen-agnostic"], "thumbnail": null, "category": "Tools", "additional_metadata": {"kind": "resource", "link": "https://github.com/genpat-it/dist2mst", "link_valid": true, "link_checked_at": "2026-09-25T10:36:06.912823"}, "page_number": 2, "directory": "hub", "items_per_page": 10}, {"src_path": "hub/tools/item-efsa-wgs-onehealth.md", "base_url": "https://globalmicrobialidentifier.org", "context_path": "hub/tools", "title": "EFSA One Health WGS analytical pipeline", "date": "2023-04-17", "description": "Nextflow pipeline used within the EFSA One Health WGS System for the collection, storage and analysis of whole genome sequencing based typing data from non-human isolates of Salmonella enterica, Listeria monocytogenes, Escherichia coli including STEC, Campylobacter jejuni and Campylobacter coli. It supports molecular surveillance and monitoring of food-borne pathogens across food, feed, animals and related environments, and underpins a system interoperable with the platform managed by ECDC, allowing the automatic exchange of typing data to support detection and investigation of multi-country food-borne outbreaks.", "terms": ["Software (Tool/Workflow)", "Microbial Typing", "Data Standardization/Harmonization", "One Health Surveillance", "Outbreak Detection/Investigation", "Pathogen-specific"], "thumbnail": null, "category": "Tools", "additional_metadata": {"kind": "resource", "link": "https://dev.azure.com/efsa-devops/EFSA/_git/efsa.wgs.onehealth", "link_valid": true, "link_checked_at": "2026-09-25T10:36:06.912823"}, "page_number": 2, "directory": "hub", "items_per_page": 10}, {"src_path": "hub/tools/item-epicollect5.md", "base_url": "https://globalmicrobialidentifier.org", "context_path": "hub/tools", "title": "Epicollect5: mobile and web application for free data collection", "date": "2009-09-16", "description": "Free and easy-to-use mobile data-gathering platform. Epicollect5 is a mobile and web application for free and easy data collection developed by the CGPS team based at the Oxford University Big Data Institute. It provides both web and mobile applications for the generation of forms (questionnaires) and freely hosted project websites for data collection. Projects are created with the web application and then downloaded to the device to perform the data collection; data are collected, including GPS and media, using multiple devices, and all data can be viewed on a central server via map, tables and charts, and exported in CSV and JSON format. The mobile app is available for Android and iOS.", "terms": ["Software (Platform)", "Sample Collection", "Data Curation", "Outbreak Detection/Investigation", "Research", "Pathogen-agnostic"], "thumbnail": null, "category": "Tools", "additional_metadata": {"kind": "resource", "link": "https://five.epicollect.net/", "link_valid": true, "link_checked_at": "2026-09-25T10:36:06.912823"}, "page_number": 3, "directory": "hub", "items_per_page": 10}, {"src_path": "hub/tools/item-galaxytrakr.md", "base_url": "https://globalmicrobialidentifier.org", "context_path": "hub/tools", "title": "GalaxyTrakr: bioinformatics platform for public health WGS analysis", "date": "2021-02-10", "description": "Customised instance of the Galaxy platform created by the Center for Food Safety and Applied Nutrition (CFSAN) of the U.S. Food and Drug Administration for laboratory scientists performing food safety regulatory work. It lets local laboratories analyse whole genome sequencing data almost directly off the sequencer, at a point where they may be best placed to intervene in an outbreak, and removes the need to master a command-line interface, so that public health scientists with molecular and microbiology backgrounds can run and interpret bioinformatics analyses themselves. Free to use after registration.", "terms": ["Software (Platform)", "Microbial Typing", "One Health Surveillance", "Outbreak Detection/Investigation", "Pathogen-agnostic"], "thumbnail": null, "category": "Tools", "additional_metadata": {"kind": "resource", "link": "https://galaxytrakr.org/", "link_valid": true, "link_checked_at": "2026-09-25T10:36:06.912823"}, "page_number": 2, "directory": "hub", "items_per_page": 10}, {"src_path": "hub/tools/item-microreact.md", "base_url": "https://globalmicrobialidentifier.org", "context_path": "hub/tools", "title": "Microreact: visualisation and sharing of data for genomic epidemiology", "date": "2016-11-30", "description": "Web-based application for the provision of interactive data visualisations, developed by the Centre for Genomic Pathogen Surveillance (CGPS). It allows users to upload, visualise and explore any combination of clustering (trees), geographic (map) and temporal (timeline) data, with other metadata variables displayed in a table and colours or shapes assigned to the map, tree and timeline. It enables the rapid generation and linkage of trees, maps, networks, charts and timelines, so that epidemiologists and key decision makers can react faster and with greater accuracy. A permanent URL is produced to share a project, or a .microreact file can be downloaded for sharing with collaborators, and views can be filtered and saved to facilitate shared understanding of complex public health data.", "terms": ["Software (Platform)", "Phylogenetic Tree Construction", "Outbreak Detection/Investigation", "Public Health Decision Making", "Knowledge Mobilization", "Pathogen-agnostic"], "thumbnail": null, "category": "Tools", "additional_metadata": {"kind": "resource", "link": "https://microreact.org/", "link_valid": true, "link_checked_at": "2026-09-25T10:36:06.912823"}, "page_number": 3, "directory": "hub", "items_per_page": 10}, {"src_path": "hub/tools/item-pathogenwatch.md", "base_url": "https://globalmicrobialidentifier.org", "context_path": "hub/tools", "title": "Pathogenwatch: genomic surveillance platform for microbial pathogens", "date": "2021-05-17", "description": "User-friendly web platform empowering researchers and public health professionals to analyse and visualise genomic data from microbial pathogens. Designed to streamline pathogen surveillance, it integrates advanced tools for resistance gene detection, lineage identification and outbreak tracking, with interactive visualisations and access to global databases. Uploaded microbial genomes initiate a suite of automated analyses and are kept private unless sharing is selected; over 20 cgMLST schemes from multiple sources and a clustering-based system identify near neighbours among extensive collections of publicly available sequences, and collections combining public and user genomes are explored through a tree panel, a map panel, data tables and a query tool.", "terms": ["Software (Platform)", "Microbial Typing", "Phylogenetic Tree Construction", "Clinical Surveillance", "Outbreak Detection/Investigation", "Public Health Decision Making", "AMR", "Pathogen-agnostic"], "thumbnail": null, "category": "Tools", "additional_metadata": {"kind": "resource", "link": "https://pathogen.watch/", "link_valid": true, "link_checked_at": "2026-09-25T10:36:06.912823"}, "page_number": 2, "directory": "hub", "items_per_page": 10}, {"src_path": "hub/tools/item-reportree.md", "base_url": "https://globalmicrobialidentifier.org", "context_path": "hub/tools", "title": "ReporTree: genetic clustering and surveillance-oriented reporting", "date": "2022-02-15", "description": "Flexible pipeline that detects pathogen genetic clusters and links them to epidemiological data, reducing the manual exploration of large phylogenetic trees to a reproducible workflow. It derives clusters at any threshold level from trees, SNP or cg/wgMLST allele matrices, VCF files, alignments or distance matrices, produces summary statistics and count matrices for the resulting clusters or any grouping variable, zooms in on samples of interest, maintains cluster nomenclature across runs with hierarchical codes, and identifies regions of cluster stability for nomenclature design.", "terms": ["Software (Tool/Workflow)", "Microbial Typing", "Phylogenetic Tree Construction", "Outbreak Detection/Investigation", "Public Health Decision Making", "Pathogen-agnostic"], "thumbnail": null, "category": "Tools", "additional_metadata": {"kind": "resource", "link": "https://github.com/insapathogenomics/ReporTree", "link_valid": true, "link_checked_at": "2026-09-25T10:36:06.912823"}, "page_number": 2, "directory": "hub", "items_per_page": 10}, {"src_path": "hub/tools/item-shovill.md", "base_url": "https://globalmicrobialidentifier.org", "context_path": "hub/tools", "title": "Shovill: fast de novo assembly of bacterial isolate genomes", "date": "2016-09-05", "description": "Pipeline that assembles bacterial isolate genomes from Illumina paired-end reads, using SPAdes at its core but reworking the steps before and after the primary assembly to reach comparable results in less time. It estimates genome size from the reads, subsamples to a sensible depth, trims adapters, corrects sequencing errors, stitches overlapping pairs, assembles with a modified kmer range, then corrects minor assembly errors and filters contigs that are too short, too low in coverage or pure homopolymers. SKESA, Velvet and Megahit are supported as alternative assemblers.", "terms": ["Software (Tool/Workflow)", "Assembly/consensus Sequence Generation", "Read Processing", "Sequence Quality Control", "Pathogen-agnostic"], "thumbnail": null, "category": "Tools", "additional_metadata": {"kind": "resource", "link": "https://github.com/tseemann/shovill", "link_valid": true, "link_checked_at": "2026-09-25T10:36:06.912823"}, "page_number": 3, "directory": "hub", "items_per_page": 10}, {"src_path": "hub/tools/item-spread.md", "base_url": "https://globalmicrobialidentifier.org", "context_path": "hub/tools", "title": "SPREAD: Spatiotemporal Pathogen Relationships and Epidemiological Analysis Dashboard", "date": "2023-08-03", "description": "Interactive web dashboard, previously known as GrapeTree Extended, that couples phylogenetic tree visualisation with an integrated GIS and a time dimension. Users can upload geographic coordinates and temporal data for each sample, cross-select between tree and map, and replay outbreak dynamics as a timelapse. It runs entirely client-side in the browser, so sensitive datasets are never transmitted. Developed by IZSAM and freely usable online or deployable locally via Docker.", "terms": ["Software (Tool/Workflow)", "Phylodynamics", "Outbreak Detection/Investigation", "One Health Surveillance", "Pathogen-agnostic"], "thumbnail": null, "category": "Tools", "additional_metadata": {"kind": "resource", "link": "https://github.com/genpat-it/spread", "link_valid": true, "link_checked_at": "2026-09-25T10:36:06.912823"}, "page_number": 2, "directory": "hub", "items_per_page": 10}]
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"hub/funding-opportunities/item-scientify-genomics.md", "title": "Genomics funding calls: live Scientify Research search", "category": "Funding opportunities", "terms": ["Costing/Funding", "Research", "Pathogen-agnostic"]}, {"src_path": "hub/scientific-papers/item-pubmed-microbial-genomics.md", "title": "Microbial bioinformatics and genomics: live PubMed search", "category": "Scientific papers", "terms": ["Research", "Pathogen-agnostic", "Knowledge Mobilization"]}, {"src_path": "hub/scientific-papers/item-pubmed-one-health-genomics.md", "title": "One Health bioinformatics and genomics: live PubMed search", "category": "Scientific papers", "terms": ["Research", "One Health Surveillance", "Pathogen-agnostic", "Knowledge Mobilization"]}, {"src_path": "hub/tools/item-cgdist.md", "title": "cgDist: SNP and InDel distance calculator for *MLST", "category": "Tools", "terms": ["Software (Tool/Workflow)", "Microbial Typing", "Variant Detection", "Outbreak Detection/Investigation", "Pathogen-agnostic"]}, {"src_path": "hub/tools/item-cgmlst-dists-py.md", "title": "cgmlst-dists-py: GPU-accelerated pairwise distance calculator for cgMLST", "category": "Tools", "terms": ["Software (Tool/Workflow)", "Microbial Typing", "Outbreak Detection/Investigation", "Pathogen-agnostic"]}, {"src_path": "hub/tools/item-chewbbaca.md", "title": "chewBBACA: cg/wgMLST schema creation and allele calling suite", "category": "Tools", "terms": ["Software (Tool/Workflow)", "Microbial Typing", "Data Standardization/Harmonization", "Outbreak Detection/Investigation", "Pathogen-agnostic"]}, {"src_path": "hub/tools/item-chewcall.md", "title": "chewcall: high-performance cgMLST and wgMLST allele caller", "category": "Tools", "terms": ["Software (Tool/Workflow)", "Microbial Typing", "Outbreak Detection/Investigation", "Pathogen-agnostic"]}, {"src_path": "hub/tools/item-cohesive.md", "title": "COHESIVE Information System (CIS)", "category": "Tools", "terms": ["Software (Platform)", "Systems 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"title": "Epicollect5: mobile and web application for free data collection", "category": "Tools", "terms": ["Software (Platform)", "Sample Collection", "Data Curation", "Outbreak Detection/Investigation", "Research", "Pathogen-agnostic"]}, {"src_path": "hub/tools/item-galaxytrakr.md", "title": "GalaxyTrakr: bioinformatics platform for public health WGS analysis", "category": "Tools", "terms": ["Software (Platform)", "Microbial Typing", "One Health Surveillance", "Outbreak Detection/Investigation", "Pathogen-agnostic"]}, {"src_path": "hub/tools/item-microreact.md", "title": "Microreact: visualisation and sharing of data for genomic epidemiology", "category": "Tools", "terms": ["Software (Platform)", "Phylogenetic Tree Construction", "Outbreak Detection/Investigation", "Public Health Decision Making", "Knowledge Mobilization", "Pathogen-agnostic"]}, {"src_path": "hub/tools/item-pathogenwatch.md", "title": "Pathogenwatch: genomic surveillance platform for microbial pathogens", "category": "Tools", "terms": ["Software (Platform)", "Microbial Typing", "Phylogenetic Tree Construction", "Clinical Surveillance", "Outbreak Detection/Investigation", "Public Health Decision Making", "AMR", "Pathogen-agnostic"]}, {"src_path": "hub/tools/item-reportree.md", "title": "ReporTree: genetic clustering and surveillance-oriented reporting", "category": "Tools", "terms": ["Software (Tool/Workflow)", "Microbial Typing", "Phylogenetic Tree Construction", "Outbreak Detection/Investigation", "Public Health Decision Making", "Pathogen-agnostic"]}, {"src_path": "hub/tools/item-shovill.md", "title": "Shovill: fast de novo assembly of bacterial isolate genomes", "category": "Tools", "terms": ["Software (Tool/Workflow)", "Assembly/consensus Sequence Generation", "Read Processing", "Sequence Quality Control", "Pathogen-agnostic"]}, {"src_path": "hub/tools/item-spread.md", "title": "SPREAD: Spatiotemporal Pathogen Relationships and Epidemiological Analysis Dashboard", "category": "Tools", "terms": ["Software (Tool/Workflow)", "Phylodynamics", "Outbreak Detection/Investigation", "One Health Surveillance", "Pathogen-agnostic"]}, {"src_path": "hub/training-resources/item-coursera-bioinformatics-genomics.md", "title": "Bioinformatics and genomics: live Coursera search", "category": "Training resources", "terms": ["Training Resource", "Knowledge Mobilization", "Pathogen-agnostic"]}, {"src_path": "hub/training-resources/item-coursera-bioinformatics-ngs.md", "title": "Bioinformatics and next-generation sequencing (NGS): live Coursera search", "category": "Training resources", "terms": ["Training Resource", "Knowledge Mobilization", "Pathogen-agnostic"]}]
GMI16 — Tunis, Tunisia, 24–25 September 2026. Follow the 16th Global Microbial Identifier Conference: programme, speakers, agenda and conference materials are published on the GMI16 page.
Global Microbial Identifier is an open community of passionate One Health professionals advancing microbial genomic surveillance and promoting microbial data sharing to create common benefits for all.
