[{"src_path": "hub/tools/item-cgdist.md", "base_url": "https://globalmicrobialidentifier.org", "context_path": "hub/tools", "title": "cgDist: SNP and InDel distance calculator for cgMLST", "date": "2025-07-26", "description": "Ultra-fast Rust implementation for calculating pairwise SNP and InDel level genetic distances from core genome MLST 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": {"link": "https://github.com/genpat-it/cgDist", "link_valid": true, "link_checked_at": "2026-09-01T13:49:01.027108"}, "page_number": 3, "directory": "hub", "items_per_page": 4}, {"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": {"link": "https://github.com/genpat-it/cgmlst-dists-py", "link_valid": true, "link_checked_at": "2026-09-01T13:49:01.027108"}, "page_number": 4, "directory": "hub", "items_per_page": 4}, {"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": {"link": "https://github.com/B-UMMI/chewBBACA", "link_valid": true, "link_checked_at": "2026-09-01T13:49:01.027108"}, "page_number": 5, "directory": "hub", "items_per_page": 4}, {"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": {"link": "https://github.com/genpat-it/chewcall", "link_valid": true, "link_checked_at": "2026-09-01T13:49:01.027108"}, "page_number": 2, "directory": "hub", "items_per_page": 4}, {"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": {"link": "https://github.com/genpat-it/cohesive", "link_valid": true, "link_checked_at": "2026-09-01T13:49:01.027108"}, "page_number": 3, "directory": "hub", "items_per_page": 4}, {"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": {"link": "https://github.com/genpat-it/dist2mst", "link_valid": true, "link_checked_at": "2026-09-01T13:49:01.027108"}, "page_number": 3, "directory": "hub", "items_per_page": 4}, {"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": {"link": "https://dev.azure.com/efsa-devops/EFSA/_git/efsa.wgs.onehealth", "link_valid": true, "link_checked_at": "2026-09-01T13:49:01.027108"}, "page_number": 4, "directory": "hub", "items_per_page": 4}, {"src_path": "hub/tools/item-efsa-wgs-reporting-guidelines.md", "base_url": "https://globalmicrobialidentifier.org", "context_path": "hub/tools", "title": "Guidelines for reporting WGS-based typing data via the EFSA WGS System", "date": "2025-12-01", "description": "EFSA guidelines for reporting whole genome sequencing based typing data through the EFSA WGS System under Commission Implementing Regulation (EU) 2025/179 and for general monitoring purposes. The platform, operational since July 2022, is part of the One Health WGS System developed by EFSA and ECDC and enables joint analysis of isolates from humans, food, feed, animals and related environments. The document describes the reporting requirements and the interoperability between the EFSA and ECDC systems, which relies on a query and response mechanism exchanging core genome MLST profiles and essential metadata.", "terms": ["Documentation", "Policy", "Data Standardization/Harmonization", "Microbial Typing", "One Health Surveillance", "Pathogen-specific"], "thumbnail": null, "category": "Tools", "additional_metadata": {"link": "https://efsa.onlinelibrary.wiley.com/doi/epdf/10.2903/sp.efsa.2025.EN-9830", "link_check": "skip", "link_checked_on": "2026-09-01", "link_valid": false, "link_checked_at": "2026-09-01T13:49:01.027108"}, "page_number": 3, "directory": "hub", "items_per_page": 4}, {"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": {"link": "https://galaxytrakr.org/", "link_valid": true, "link_checked_at": "2026-09-01T13:49:01.027108"}, "page_number": 5, "directory": "hub", "items_per_page": 4}, {"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": {"link": "https://github.com/insapathogenomics/ReporTree", "link_valid": true, "link_checked_at": "2026-09-01T13:49:01.027108"}, "page_number": 4, "directory": "hub", "items_per_page": 4}, {"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": {"link": "https://github.com/tseemann/shovill", "link_valid": true, "link_checked_at": "2026-09-01T13:49:01.027108"}, "page_number": 5, "directory": "hub", "items_per_page": 4}, {"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": {"link": "https://github.com/genpat-it/spread", "link_valid": true, "link_checked_at": "2026-09-01T13:49:01.027108"}, "page_number": 4, "directory": "hub", "items_per_page": 4}]
[{"src_path": "hub/funding-opportunities/item-scientify-genomics-bioinformatics.md", "title": "Genomics and bioinformatics funding calls: live Scientify Research search", "category": "Funding opportunities", "terms": ["Costing/Funding", "Research", "Bioinformatics Protocols", "Pathogen-agnostic"]}, {"src_path": "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 cgMLST", "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 Development", "One Health Surveillance", "Outbreak Detection/Investigation", "Pathogen-agnostic"]}, {"src_path": "hub/tools/item-dist2mst.md", "title": "dist2mst: Minimum Spanning Tree construction from distance matrices", "category": "Tools", "terms": ["Software (Tool/Workflow)", "Phylogenetic Tree Construction", "Outbreak Detection/Investigation", "Pathogen-agnostic"]}, {"src_path": "hub/tools/item-efsa-wgs-onehealth.md", "title": "EFSA One Health WGS analytical pipeline", "category": "Tools", "terms": ["Software (Tool/Workflow)", "Microbial Typing", "Data Standardization/Harmonization", "One Health Surveillance", "Outbreak Detection/Investigation", "Pathogen-specific"]}, {"src_path": "hub/tools/item-efsa-wgs-reporting-guidelines.md", "title": "Guidelines for reporting WGS-based typing data via the EFSA WGS System", "category": "Tools", "terms": ["Documentation", "Policy", "Data Standardization/Harmonization", "Microbial Typing", "One Health Surveillance", "Pathogen-specific"]}, {"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-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 registration is open. Join scientists, public health professionals, veterinarians, food safety experts, environmental specialists, policy makers and industry partners in Tunis, Tunisia, for the 16th Global Microbial Identifier Conference on 24–25 September 2026.
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.
