This page captures all tools and resources mentioned across the Infectious Diseases Toolkit.
| Tool or resource | Description | Related pages | Registry |
|---|---|---|---|
| 1+ Million Genomes (1+MG) | The 1+ Million Genomes (1+MG) initiative aims to enable secure access to genomics and the corresponding clinical data across Europe for better research, personalised healthcare and health policy making. Since the Digital Day 2018, 25 EU countries, the UK and Norway signed Member States declaration on stepping up efforts towards creating a European data infrastructure for genomic data and implementing common national rules enabling federated data access. The initiative forms part of the EU's agenda for the Digital Transformation of Health and Care and is aligned with the goals of the European Health Data Space. | Training | |
| ABRicate | ABRicate is used for mass screening of contigs for antimicrobial resistance or virulence genes. | Pathogen characterisation | Tool info Training |
| ACE Cohort | Asymptomatic COVID-19 in Education (ACE) Cohort | Human biomolecular data | Training |
| ADA-M | Responsible sharing of biomedical data and biospecimens via the Automatable Discovery and Access Matrix (ADA-M). The Automatable Discovery and Access Matrix (ADA-M) provides a standardized way to unambiguously represent the conditions related to data discovery and access. By adopting ADA-M, data custodians can generally describe what their data are (the Header section), who can access them (the Permissions section), terms related to their use (the Terms section), and special conditions (the Meta-Conditions). By doing so, data custodians can participate in data sharing and collaboration by making meta information about their data computer-readable and hence directly available for digital communication, searching and automation activities. | Human biomolecular data | Tool info |
| AgrVATE | AgrVATE is a tool for rapid identification of Staphylococcus aureus agr locus type and also reports possible variants in the agr operon. | Pathogen characterisation | Tool info |
| AMRfinderplus | NCBI Antimicrobial Resistance Gene Finder (AMRFinderPlus) | Pathogen characterisation | Tool info |
| ANNOVAR | ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes. | Human biomolecular data Pathogen characterisation | Tool info |
| apex | Absolute protein expression Quantitative Proteomics Tool, is a free and open source Java implementation of the APEX technique for the quantitation of proteins based on standard LC- MS/MS proteomics data. | Pathogen characterisation | Tool info |
| ARIBA | ARIBA is an Antimicrobial Resistance Identification By Assembly | Pathogen characterisation | |
| ArrayExpress | ArrayExpress is a database of functional genomics experiments that can be queried and the data downloaded. It includes gene expression data from microarray and high throughput sequencing studies. Data is collected to MIAME and MINSEQE standards. Experiments are submitted directly to ArrayExpress or are imported from the NCBI GEO database. | Human biomolecular data Linked pathogen and ho... | Tool info Standards/Databases Training |
| artic | artic is a pipeline and set of accompanying tools for working with viral nanopore sequencing data, generated from tiling amplicon schemes. | Pathogen characterisation | Tool info Standards/Databases Training |
| Arvados | With Arvados, bioinformaticians run and scale compute-intensive workflows, developers create biomedical applications, and IT administrators manage large compute and storage resources. | Human biomolecular data | |
| Bakta | Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs. | Pathogen characterisation | Tool info Training |
| Bcftools | Bcftools is a set of tools for working with variant calls in the VCF format. | Pathogen characterisation Human biomolecular data | Tool info Training |
| Beacon v2 | Beacon v2 is a protocol/specification established by the Global Alliance for Genomics and Health initiative (GA4GH) that defines an open standard for federated discovery of genomic data and associated information in biomedical research and clinical applications. | Human biomolecular data Human clinical and hea... | Tool info Standards/Databases Training |
| BEAST | BEAST is a cross-platform program for Bayesian phylogenetic analysis, estimating rooted, time-measured phylogenies using strict or relaxed molecular clock models. It uses Markov chain Monte Carlo (MCMC) to average over tree space and includes a graphical user interface for setting up analyses and tools for result analysis. | Pathogen characterisation | Tool info |
| BEAUti | BEAUti is a graphical user-interface (GUI) application for generating BEAST XML files. | Pathogen characterisation | |
| Bento platform | The Bento platform enables the research community to explore the BQC19 cohort aggregate data. | Human biomolecular data | |
| Beyond 1 Million Genomes (B1MG) | The Beyond 1 Million Genomes (B1MG) project is helping to create a network of genetic and clinical data across Europe. The project provides coordination and support to the 1+ Million Genomes Initiative (1+MG). This initiative is a commitment of 24 EU countries, the UK and Norway to give cross-border access to one million sequenced genomes by 2022. | ||
| BioGRID | BioGRID is a comprehensive biomedical repository for curated protein, genetic and chemical interactions | Human biomolecular data Pathogen characterisation | Tool info Standards/Databases |
| BioPortal | A comprehensive repository of biomedical ontologies | Human clinical and hea... | Tool info Standards/Databases Training |
| BioSamples | BioSamples stores and supplies descriptions and metadata about biological samples used in research and development by academia and industry. Samples are either 'reference' samples (e.g. from 1000 Genomes, HipSci, FAANG) or have been used in an assay database such as the European Nucleotide Archive (ENA) or ArrayExpress. It provides links to assays and specific samples, and accepts direct submissions of sample information. | Human biomolecular data Linked pathogen and ho... | Tool info Standards/Databases Training |
| BioStudies | The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication. | FAIR data Linked pathogen and ho... | Tool info Standards/Databases Training |
| Bismark | Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step. | Human biomolecular data | Tool info Training |
| Bitbucket | Git based code hosting and collaboration tool, built for teams. | Human biomolecular data Pathogen characterisation | Standards/Databases |
| Bowtie2 | Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. | Human biomolecular data Pathogen characterisation | Tool info Training |
| BWA | BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome. | Human biomolecular data Pathogen characterisation | Tool info Training |
| C-WAP | CFSAN Wastewater Analysis Pipeline to estimate the percentage of SARS-CoV-2 variants in a sample. | Pathogen characterisation | |
| camflow | CamFlow is a Linux Security Module (LSM) designed to capture data provenance for the purpose of system audit | General guidelines | |
| Canu | Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing. | Human biomolecular data Pathogen characterisation | Tool info |
| CellDesigner | CellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical networks. | Pathogen characterisation | |
| Centrifuge | Tool to classify the taxonomic origin of a read in pathogen sequencing data | Pathogen characterisation Human biomolecular data | Tool info |
| CESSDA Data Catalogue (CDC) | CDC is a one-stop shop for searching and finding European social science data. | Socioeconomic data | Tool info Standards/Databases |
| CESSDA Vocabulary Service | CESSDA Vocabulary Service enables users to discover, browse, and download controlled vocabularies in a variety of languages. The service is provided by the Consortium of European Social Science Data Archives (CESSDA). The majority of the source (English) vocabularies included in the service have been created by the DDI Alliance. The Data Documentation Initiative (DDI) is an international standard for describing data produced by surveys and other observational methods in the social, behavioural, economic, and health sciences. | Standards/Databases | |
| Chenomx | A commercial software package for NMR spectral processing that offers a semi-automated tool for spectral deconvolution, enabling interactive fitting of metabolite peaks to reference spectra and quantifying their concentrations. | Pathogen characterisation | |
| chewBBACA | chewBBACA is a software suite for the creation and evaluation of core genome and whole genome MultiLocus Sequence Typing (cg/wgMLST) schemas and results. | Pathogen characterisation | Tool info |
| Clark | Clark is a fast, versatile and accurate tool for sequence classification system | Pathogen characterisation | Tool info Training |
| ClustalW | ClustalW is a progressive multiple sequence alignment tool to align a set of sequences by repeatedly aligning pairs of sequences and previously generated alignments. | Human biomolecular data Pathogen characterisation | Tool info Training |
| COJAC | The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. | Pathogen characterisation | Tool info |
| CoMet | A workflow using contig coverage and composition for binning a metagenomic sample with high precision | Pathogen characterisation | Tool info |
| Common Workflow Language (CWL) | An open standard for describing workflows that are build from command line tools | General guidelines Human clinical and hea... | Standards/Databases Training |
| COMPSs | COMP Superscalar (COMPSs) is a task-based programming model which aims to ease the development of applications for distributed infrastructures, such as large High-Performance clusters (HPC), clouds and container managed clusters. | General guidelines Human clinical and hea... | Tool info |
| COVID-19 BEACON | The COVID-19 Beacon is a searchable platform for SARS-CoV-2 genomic variants conforming to the Beacon specifications of the Global Alliance for Genomics and Health but adjusted for viral genome searches. | Human biomolecular data | |
| COVID-19 Data Portal | The COVID-19 Data Portal enables researchers to upload, access and analyse COVID-19 related reference data and specialist datasets. The aim of the COVID-19 Data Portal is to facilitate data sharing and analysis, and to accelerate coronavirus research. The portal includes relevant datasets submitted to EMBL-EBI as well as other major centres for biomedical data. The COVID-19 Data Portal is the primary entry point into the functions of a wider project, the European COVID-19 Data Platform. | FAIR data Human biomolecular data Human clinical and hea... Socioeconomic data The Swedish Pathogens ... | Tool info Standards/Databases Training |
| COVID19 Disease Map | The COVID-19 Disease Map is an assembly of molecular interaction diagrams, established based on literature evidence. | Pathogen characterisation | |
| COWWID | A GitHub repository from the CBG-ETHZ group offering tools for detecting SARS-CoV-2 variants in Switzerland. | ||
| CRG COVID-19 Viral Beacon | A platform allowing for browsing SARS-CoV-2 variability at the genome, amino acid, structural, and motif levels | Human biomolecular data An automated SARS-CoV-... | |
| Cromwell | Cromwell is a Workflow Management System geared towards scientific workflows. | Human biomolecular data | |
| CS_Score | R package for cell-type-specific co-expression inference from single cell RNA-sequencing data. | Human biomolecular data | |
| Cutadapt | Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. | Pathogen characterisation | Tool info Training |
| cwltool | Reference implementation to provide comprehensive validation of CWL files as well as provide other tools related to working with CWL. | Human biomolecular data | |
| Cytoscape | Cytoscape provides a solid platform for network visualization and analysis | Human biomolecular data Pathogen characterisation | Tool info Training |
| DAGitty | DAGitty is a browser-based environment for creating, editing, and analyzing causal diagrams (also known as directed acyclic graphs or causal Bayesian networks). | Prototyping federated ... | Tool info Standards/Databases |
| Danish Research Health Data Gateway | Tool that provides the user with an overview of available health data in Denmark and the entire application process, from initial idea to final application. | Human clinical and hea... | |
| Data Structure Wizard (DSW) | The Data Structure Wizard (DSW) is a Java standalone desktop application that supports version 2.0 & 2.1 of the SDMX standard. | Socioeconomic data | |
| data.validator R package | Validate dataset by columns and rows using convenient predicates inspired by 'assertr' package. | Socioeconomic data | |
| DAVID | The Database for Annotation, Visualization and Integrated Discovery (DAVID) provides a comprehensive set of functional annotation tools for investigators to understand the biological meaning behind large lists of genes. | Human biomolecular data | Tool info Training |
| dbGaP | The Database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype. Such studies include genome-wide association studies, medical sequencing, molecular diagnostic assays, as well as association between genotype and non-clinical traits. | FAIR data Human biomolecular data | Tool info Standards/Databases Training |
| dbNSFP | A comprehensive database of transcript-specific functional predictions and annotations for human non-synonymous and splice-site SNVs | Human biomolecular data Pathogen characterisation | Tool info |
| DCAT | An RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web. By using DCAT to describe datasets in data catalogs, publishers increase discoverability and enable applications easily to consume metadata from multiple catalogs. | Human clinical and hea... Human biomolecular data | Standards/Databases |
| DDI Tools | Searchable list of tools available to help you work with DDI, from authoring and editing metadata to data transformations. The tools have been developed independently by a variety of organizations from the global DDI community. | ||
| DeconSeq | Tool to remove human reads from pathogen sequencing data. | Human biomolecular data | Tool info |
| dedupe | Python library that uses machine learning to perform fuzzy matching, deduplication, and entity resolution quickly on structured data. | Socioeconomic data | Training |
| DeepVariant | DeepVariant is a deep learning-based variant caller that takes aligned reads (in BAM or CRAM format), produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports the results in a standard VCF or gVCF file. | Human biomolecular data | Tool info |
| Delly | Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read and long-read massively parallel sequencing data. | Human biomolecular data | Tool info |
| DESeq2 | Differential gene expression analysis based on the negative binomial distribution | Human biomolecular data Pathogen characterisation | Tool info Training |
| DFAST | DFAST is a flexible and customizable pipeline for prokaryotic genome annotation as well as data submission to the INSDC | Pathogen characterisation | Tool info |
| DIAMOND | DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data. | Pathogen characterisation | Tool info Training |
| dlookr | A collection of tools that support data diagnosis, exploration, and transformation. | Socioeconomic data | |
| Docker | Docker is a software for the execution of applications in virtualized environments called containers. It is linked to DockerHub, a library for sharing container images | Human biomolecular data | Standards/Databases Standards/Databases Training |
| Dorado | Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. | Pathogen characterisation | Tool info |
| dplyr | dplyr is a grammar of data manipulation, providing a consistent set of verbs that help you solve the most common data manipulation challenges. | Socioeconomic data Socioeconomic data | Training |
| Dragen-GATK | DRAGEN-GATK Best Practices contains open-source workflows that are compatible between Illumina's platforms and mainstream infrastructure. | Human biomolecular data Pathogen characterisation | |
| Dragonflye | Dragonflye is a pipeline that aims to make assembling Oxford Nanopore reads quick and easy. | Pathogen characterisation | |
| Dryad | Dryad is an open-source, community-led data curation, publishing, and preservation platform for CC0 publicly available research data. | Human biomolecular data | Standards/Databases |
| dupRadar | dupRadar is used for the assessment of duplication rates in RNA-Seq datasets. | Pathogen characterisation | Tool info |
| Dutch COVID-19 Data Portal | The dutch COVID-19 Data Portal provides researchers with a clear overview of what is available, allow searching for specific data and make access to such data easier when the necessary ethical and legal conditions have been met. | Human biomolecular data | |
| EBI | The European Bioinformatics Institute is a bioinformatics research center that is part of the European Molecular Biology Laboratory and is located in Hinxton, England. The institution combines intense research activity with the development and maintenance of a set of bioinformatics lines, services and databases. | Human biomolecular data | Training |
| ECTyper | ECTyper is a standalone versatile serotyping module for Escherichia coli. It supports both fasta (assembled) and fastq (raw reads) file formats. | Pathogen characterisation | Tool info |
| EdgeR | Empirical Analysis of Digital Gene Expression Data in R | Human biomolecular data | Tool info Training |
| EGA Beacon | Interface to query on the EGA data through Beacon v2 | Human biomolecular data | |
| emmtyper | emmtyper is a command line tool for emm-typing of Streptococcus pyogenes using a de novo or complete assembly. | Pathogen characterisation | Tool info |
| ENA upload CLI | Command line tool (CLI) allowing easy submission of data and respective metadata to the European Nucleotide Archive (ENA) using tabular files or an excel spreadsheet. The tool allows programatic submission of all ENA objects (study, sample, run and experiment) without the need of logging in to the Webin interface. This also includes client side validation using ENA checklists and releasing the ENA objects. | Using the ENA data sub... SARS-CoV-2 sequencing ... | |
| ENA upload Galaxy tool | Galaxy tool wrapper of the ENA upload CLI to submit experimental data and respective metadata to the European Nucleotide Archive (ENA). | Using the ENA data sub... SARS-CoV-2 sequencing ... | |
| ENA Webin CLI | Galaxy wrapper to submit consensus sequences to ENA in an interactive way. The tool has the Webin-CLI script of ENA at its core and supports all sample checklists. | Using the ENA data sub... | |
| Enrichr | Functional Enrichment Analysis and Network Construction | Pathogen characterisation | Tool info |
| Estonian Biobank | The Estonian Biobank has established a population-based biobank of Estonia with a current cohort size of more than 200,000 individuals (genotyped with genome-wide arrays), reflecting the age, sex and geographical distribution of the adult Estonian population. Considering the fact that about 20% of Estonia's adult population has joined the programme, it is indeed a database that is very important for the development of medical science both domestically and internationally. | Human biomolecular data | |
| Estonian COVID-19 Data Portal | Estonian instance of the COVID-19 Data Portal. Among other information, served Estonian SARS-CoV-2 sequencing dashboards. | SARS-CoV-2 sequencing ... The Swedish Pathogens ... | |
| EUI COVID-19 SSH Data Portal | The COVID-19 SSH Data Portal provides integrated search, discovery, and linking to datasets published on the web relevant for COVID-19-related research in the Social Sciences and Humanities. | Socioeconomic data | Standards/Databases |
| EuroHPC | EuroHPC Joint Undertaking is a joint initiative between the EU, European countries and private partners to develop a World Class Supercomputing Ecosystem in Europe. | Pathogen characterisation | |
| European Centre for Disease Prevention and Control (ECDC) | It is an EU agency aimed at strengthening Europe's defences against infectious diseases. Their mission is to identify, assess and communicate current and emerging threats to human health posed by infectious diseases. | Human clinical and hea... | |
| European Clinical Research Infrastructure Network (ECRIN) tools | ECRIN develops, contributes to, and maintains freely accessible tools that facilitate the identification of clinical trial objects, data sharing, access to regulatory and methodological designs and much more to support researchers looking to conduct multinational clinical research. | Human clinical and hea... | |
| European Genome-phenome Archive (EGA) | The European Genome-phenome Archive (EGA) is a service for permanent archiving and sharing of personally identifiable genetic, phenotypic, and clinical data generated for the purposes of biomedical research projects or in the context of research-focused healthcare systems. Access to data must be approved by the specified Data Access Committee (DAC). | FAIR data Human biomolecular data Human clinical and hea... Linked pathogen and ho... | Tool info Standards/Databases Training |
| European Health Data Space (EHDS) | The European Health Data Space is a health specific ecosystem comprised of rules, common standards and practices, infrastructures and a governance framework that aims at empowering individuals through increased digital access to and control of their electronic personal health data, at national level and EU-wide. | Human clinical and hea... Human clinical and hea... | |
| European Health Information Portal | The Health Information Portal provides access to population health and healthcare data across Europe. | FAIR data Human clinical and hea... | Standards/Databases |
| European Language Social Science Thesaurus (ELSST) | The European Language Social Science Thesaurus (ELSST) is a broad-based, multilingual thesaurus for the social sciences. It is owned and published by the Consortium of European Social Science Data Archives (CESSDA) and its national Service Providers. | Standards/Databases | |
| European Medicines Agency (EMA) | The European Medicines Agency (EMA) is a decentralised agency of the European Union (EU). It is responsible for the scientific evaluation, supervision and safety monitoring of medicines. | Human clinical and hea... | |
| European Nucleotide Archive (ENA) | Provides a record of the nucleotide sequencing information. It includes raw sequencing data, sequence assembly information and functional annotation. | Pathogen characterisation Human clinical and hea... Pathogen characterisation Human biomolecular data An automated SARS-CoV-... Using the ENA data sub... SARS-CoV-2 sequencing ... Linked pathogen and ho... | Tool info Standards/Databases Training |
| FAIRsharing | FAIRsharing is a FAIR-supporting resource that provides an informative and educational registry on data standards, databases, repositories and policy, alongside search and visualization tools and services that interoperate with other FAIR-enabling resources. FAIRsharing guides consumers to discover, select and use standards, databases, repositories and policy with confidence, and producers to make their resources more discoverable, more widely adopted and cited. Each record in fairsharing is curated in collaboration with the maintainers of the resource themselves, ensuring that the metadata in the fairsharing registry is accurate and timely. | Pathogen characterisation Human biomolecular data Ethical, Legal, and So... | Standards/Databases Training |
| fastp | A tool designed to provide ultrafast all-in-one preprocessing and quality control for FastQ data. | Pathogen characterisation | Tool info Training |
| FASTQC | A quality control tool for high throughput sequence data. | Pathogen characterisation Human biomolecular data Pathogen characterisation | Tool info Training |
| FastQC Screen | FastQ Screen is a quality control tool used to detect contamination in sequencing data (FASTQ files). | Human biomolecular data | |
| FastTree | FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences | Pathogen characterisation | Tool info Training |
| Federated EGA | The Federated EGA is an infrastructure built upon the European Genome-phenome Archive (EGA), an EMBL-EBI and CRG data resource for secure archiving and sharing of human sensitive biomolecular and phenotypic data resulting from biomedical research projects. | Human biomolecular data Human clinical and hea... | Training |
| Figshare | Figshare is a generalist, subject-agnostic repository for many different types of digital objects that can be used without cost to researchers. Data can be submitted to the central figshare repository (described here), or institutional repositories using the figshare software can be installed locally, e.g. by universities and publishers. | Human biomolecular data | Standards/Databases Training |
| Findata | Findata is the data permit authority for the social and health care sector in Finland. | Human clinical and hea... | |
| FluServer | The main application scenario for FluSurver is to highlight phenotypically or epidemiologically interesting candidate mutations for further research and should ideally be combined with experimental testing and verification of any predicted phenotypes. | Pathogen characterisation | |
| Flye | Flye is a de novo assembler for single-molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. | Human biomolecular data Pathogen characterisation | Tool info Training |
| freebayes | freebayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, MNPs, and complex events smaller than the length of a short-read sequencing alignment. | Human biomolecular data Pathogen characterisation | Tool info Training |
| French Health Data Hub | French Health Data Hub that guarantees easy and unified, transparent and secure access to health data to improve the quality of care and patient support. | Human clinical and hea... | |
| Freyja | Freyja is a tool to recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset (BAM aligned to the Hu-1 reference). | Pathogen characterisation | Tool info |
| g:Profiler | g:GOSt performs functional enrichment analysis, also known as over-representation analysis (ORA) or gene set enrichment analysis, on input gene list. | Pathogen characterisation | Tool info Training |
| Galaxy | Open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses. | Human biomolecular data Pathogen characterisation General guidelines Human clinical and hea... Using the ENA data sub... | Tool info Training |
| Galaxy Europe | The European Galaxy server. Provides access to thousands of tools for scalable and reproducible analysis. | Pathogen characterisation An automated SARS-CoV-... | Training |
| Galaxy University of Tartu | The University of Tartu Galaxy instance. Enables local university users to run their analyses in the Galaxy environment. Was heavily used during the KoroGenoEST sequencing studies. | SARS-CoV-2 sequencing ... | |
| Ganon | ganon2 classifies DNA sequences against large sets of genomic reference sequences efficiently. | Pathogen characterisation | Tool info |
| GenBank | GenBank is the NIH genetic sequence database of annotated collections of all publicly available DNA sequences. | Human biomolecular data | Tool info Standards/Databases Training |
| GenCoF | Tool to remove human reads from pathogen sequencing data | Human biomolecular data | |
| GeneMANIA | GeneMANIA helps you predict the function of your favourite genes and gene sets. | Human biomolecular data | Tool info Training |
| Geno2pheno | Estimating phenotypic drug resistance from HIV-1 genotypes associated with resistance to PRO and RT inhibitors | Pathogen characterisation | Tool info |
| Genome Analysis Toolkit (GATK) | GATK is a widely used tool for variant calling and genotyping from NGS data. | Human biomolecular data | Tool info |
| Genome Detective | Genome Detective offers intuitive Bio-Informatics applications for the analysis of microbial molecular sequence data. | Pathogen characterisation | |
| Genomic Data Infrastructure (GDI) | The Genomic Data Infrastructure (GDI) project is enabling access to genomic and related phenotypic and clinical data across Europe. It is doing this by establishing a federated, sustainable and secure infrastructure to access the data. It builds on the outputs of the Beyond 1 Million Genomes (B1MG) project and is realising the ambition of the 1+Million Genomes (1+MG) initiative. | ||
| Genotype-Tissue Expression (GTEx) | The Genotype-Tissue Expression (GTEx) project is an ongoing effort to build a comprehensive public resource to study tissue-specific gene expression and regulation. Samples were collected from 53 non-diseased tissue sites across nearly 1000 individuals, primarily for molecular assays including WGS, WES, and RNA-Seq. Remaining samples are available from the GTEx Biobank. The GTEx Portal provides open access to data including gene expression, QTLs, and histology images. | Human biomolecular data | Tool info Standards/Databases |
| GEO | The Gene Expression Omnibus (GEO) is a public repository that archives and freely distributes microarray, next-generation sequencing, and other forms of high-throughput functional genomic data submitted by the scientific community. Accepts next generation sequence data that examine quantitative gene expression, gene regulation, epigenomics or other aspects of functional genomics using methods such as RNA-seq, miRNA-seq, ChIP-seq, RIP-seq, HiC-seq, methyl-seq, etc. GEO will process all components of your study, including the samples, project description, processed data files, and will submit the raw data files to the Sequence Read Archive (SRA) on the researchers behalf. In addition to data storage, a collection of web-based interfaces and applications are available to help users query and download the studies and gene expression patterns stored in GEO. | Human biomolecular data | Standards/Databases Training |
| ggplot2 | ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics. | Human biomolecular data | Tool info Training |
| GitHub | GitHub is a versioning system, used for sharing code, as well as for sharing of small data. | Human biomolecular data Pathogen characterisation An automated pipeline ... | Standards/Databases Standards/Databases Training |
| GitLab | GitLab is an open source end-to-end software development platform with built-in version control, issue tracking, code review, CI/CD, and more. Self-host GitLab on your own servers, in a container, or on a cloud provider. | Human biomolecular data Pathogen characterisation | Standards/Databases Training |
| Global Alliance for Genomics and Health (GA4GH) | The metadata model for GA4GH, an international coalition of both public and private interested parties, formed to enable the sharing of genomic and clinical data. | Human biomolecular data | Tool info Standards/Databases Training |
| Global Initiative on Sharing All Influenza Data (GISAID) | A web-based platform for sharing viral sequence data, initially for influenza data, and now for other pathogens (including SARS-CoV-2). | Pathogen characterisation Human clinical and hea... Pathogen characterisation | Standards/Databases |
| GO | GO is to perform enrichment analysis on gene sets. | Human biomolecular data Pathogen characterisation | Tool info Training |
| GRAF pop | GRAF pop is a software tool that infers the subject ancestry. | Human biomolecular data | |
| GRAF sex | Tool that determines subject sexes using the genotypes. | Human biomolecular data | |
| GRIDSS | GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. | Human biomolecular data | Tool info |
| GSEA | Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states | Human biomolecular data | Tool info Training |
| Guppy | Guppy is a bioinformatics toolkit that enables real-time basecalling and several post-processing features that works on Oxford Nanopore Technologies™ sequencing platforms. | Pathogen characterisation | Tool info |
| hAMRonization | hAMRonization is a software tool to harmonize and standardize antimicrobial resistance (AMR) data generated by various bioinformatics tools. | Pathogen characterisation | Tool info |
| HCV-GLUE | HCV-GLUE is a bioinformatics resource for HCV sequence data. | Pathogen characterisation | |
| Health Research Data UK | HDR UK is a national institute with the aim to unite the UK’s health and care data to enable discoveries that improve people’s lives. We do this by uniting, improving and using health and care data as one national institute. | Human clinical and hea... | |
| hicap | The cap locus of H. influenzae are categorised into 6 different groups based on serology (a-f). | Pathogen characterisation | |
| HISAT2 | HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (whole-genome, transcriptome, and exome sequencing data) to a population of human genomes (as well as to a single reference genome). | Human biomolecular data Pathogen characterisation | Tool info Training |
| IGV | The Integrative Genomics Viewer (IGV) is a high-performance, easy-to-use, interactive tool for the visual exploration of genomic data. | Human biomolecular data | Tool info Training |
| IntAct | IntAct (Molecular Interaction Database) Website | Human biomolecular data Pathogen characterisation | Tool info Standards/Databases Training |
| IQtree | IQ-TREE is designed to efficiently handle large phylogenomic datasets, utilize multicore and distributed parallel computing for faster analysis, and automatically resume interrupted analyses through checkpointing. | Pathogen characterisation | Tool info Training |
| IRMA | IRMA (Iterative Refinement Meta-Assembler) was designed for the robust assembly, variant calling, and phasing of highly variable RNA viruses. | Pathogen characterisation | Tool info |
| ISARIC COVID-19 Case Report Form | The ISARIC-WHO Case Report Forms (CRFs) should be used to collect data on individuals presenting with suspected or confirmed COVID-19, with the aim to standardise clinical data to improve patient care and inform the public health response. | Linked pathogen and ho... | Standards/Databases |
| iVar | iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing. | Pathogen characterisation | Tool info Training |
| Kaiju | Kaiju is a program for the taxonomic classification of high-throughput sequencing reads, e.g., Illumina or Roche/454, from whole-genome sequencing of metagenomic DNA. | Pathogen characterisation | Tool info |
| Kallisto | Kallisto is a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. | Pathogen characterisation | Tool info |
| KEGG | A set of annotation maps for Kyoto encyclopedia of genes and genomes (KEGG) | Human biomolecular data | Tool info Training |
| Kleborate | Kleborate was primarily developed to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC). | Pathogen characterisation | Tool info |
| KMCP | KMCP is an accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping | Pathogen characterisation | |
| KmerFinder | KmerFinder is a bioinformatics tool designed for the rapid identification of bacterial species and strains from whole genome sequencing (WGS) data. | Pathogen characterisation | Tool info |
| Kraken | Tool to classify the taxonomic origin of a read in pathogen sequencing data. | Human biomolecular data | Tool info Training |
| Kraken 2 | A taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. | Pathogen characterisation | |
| KrakenUniq | False-positive identifications are a significant problem in metagenomics classification. | Pathogen characterisation | Tool info |
| Krona Tools | Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files. | Pathogen characterisation | Tool info |
| legsta | In silico Legionella pneumophila Sequence Based Typing (SBT). | Pathogen characterisation | Tool info |
| LimeSurvey | LimeSurvey is a free and open source advanced online survey system to create online surveys. | ||
| Lineagespot | Lineagespot is a framework written in R, and aims to identify SARS-CoV-2 related mutations based on a single (or a list) of variant(s) file(s). | Pathogen characterisation | Tool info |
| LisSero | In silico serogroup typing prediction for Listeria monocytogenes | Pathogen characterisation | |
| LoFreq* | LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data | Pathogen characterisation | Training |
| LongQC | LongQC is a tool for the data quality control of the PacBio and ONT long reads, and it has two functionalities: sample qc and platform qc. | Pathogen characterisation | |
| Lumpy | A probabilistic framework for structural variant discovery. | Human biomolecular data | Tool info |
| MACS | Model-based Analysis of ChIP-Seq (MACS), for identifying transcript factor binding sites. | Human biomolecular data | Tool info Training |
| MAFFT | MAFFT is a multiple sequence alignment program | Human biomolecular data Pathogen characterisation | Tool info Training |
| Manta | Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. | Human biomolecular data | Tool info |
| matplotlib | Matplotlib is a comprehensive library for creating static, animated, and interactive visualizations in Python. | Human biomolecular data Socioeconomic data | Tool info Training |
| MAXQUANT | MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. | Pathogen characterisation | Tool info Training |
| Medaka | medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. | Pathogen characterisation | Tool info Standards/Databases Training |
| MEGAHIT | MEGAHIT is an ultra-fast and memory-efficient NGS assembler optimized for metagenomes. | Pathogen characterisation | Tool info Training |
| MEGAN | MEGAN is used fot the interactive exploration and analysis of large-scale microbiome sequencing data. | Pathogen characterisation | Tool info |
| meningotype | In silico typing of Neisseria meningitidis contigs. | Pathogen characterisation | Tool info |
| MetaboAnalyst | MetaboAnalyst is a comprehensive platform dedicated for metabolomics data analysis via user-friendly, web-based interface. | Human biomolecular data Pathogen characterisation | Tool info Training |
| Metagen-FastQC | Cleans metagenomic reads to remove adapters, low-quality bases and host (e.g. human) contamination. | Using the ENA data sub... SARS-CoV-2 sequencing ... | |
| MetaGeniE | Tool to remove human reads from pathogen sequencing data. | Human biomolecular data | |
| MetaPhlAn | MetaPhlAn is a computational tool for species-level microbial profiling (bacteria, archaea, eukaryotes, and viruses) from metagenomic shotgun sequencing data. | Pathogen characterisation | Tool info Training |
| MethylKit | methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. | Human biomolecular data | Tool info |
| methylPipe | Base resolution DNA methylation data analysis | Human biomolecular data | Tool info |
| MetSign | A computational platform for high-resolution mass spectrometry-based metabolomics | Human biomolecular data | |
| MIABIS | MIABIS represents the minimum information required to initiate collaborations between biobanks and to enable the exchange of biological samples and data. The aim is to facilitate the reuse of bio-resources and associated data by harmonizing biobanking and biomedical research. | Human biomolecular data | Standards/Databases |
| mice | Multiple imputation using Fully Conditional Specification (FCS) implemented by the MICE algorithm as described in Van Buuren and Groothuis-Oudshoorn (2011) <doi:10.18637/jss.v045.i03>. | Socioeconomic data | Training |
| Miniasm | Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. | Pathogen characterisation | Tool info Training |
| Minimap2 | Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database. | Pathogen characterisation | Tool info Training |
| MinIONQC | Fast and effective quality control for MinION and PromethION sequencing data | Pathogen characterisation | |
| missingno | missingno provides a small toolset of flexible and easy-to-use missing data visualizations and utilities that allows you to get a quick visual summary of the completeness (or lack thereof) of your dataset. | Socioeconomic data | |
| missMethods | Supply functions for the creation and handling of missing data as well as tools to evaluate missing data methods | Socioeconomic data | |
| mOTUs | The mOTU profiler is a computational tool that estimates relative taxonomic abundance of known and currently unknown microbial community members using metagenomic shotgun sequencing data. | Pathogen characterisation | Tool info Training |
| Mouse Brain Alignment Tool (MBAT) | Semi-automated processing of autoradiography (ARG) images from mouse brain tissue. This project includes a Napari-based user interface where ARG slides can be preprocessed and registered to Allen Brain Atlas regions. | An automated pipeline ... | |
| MrBayes | MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters. | Pathogen characterisation | Tool info |
| MTBseq | MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from Illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates. | Pathogen characterisation | |
| MultiQC | MultiQC searches a given directory for analysis logs and compiles a HTML report. | Pathogen characterisation Pathogen characterisation | Tool info Training |
| MUSCLE | MUSCLE is widely-used software for making multiple alignments of biological sequences. | Human biomolecular data Pathogen characterisation | Tool info Training |
| Mzmine | MZmine 3 is an open-source software for mass-spectrometry data processing, with the main focus on LC-MS data. | Human biomolecular data Pathogen characterisation | Tool info |
| naniar | The package naniar is used for exploring missing data structures with minimal deviation from the common workflows of ggplot and tidy data (Wickham, 2014, Wickham, 2009). | Socioeconomic data | |
| NanoCaller | NanoCaller is a computational method that integrates long reads in deep convolutional neural network for the detection of SNPs/indels from long-read sequencing data. | Pathogen characterisation | Tool info |
| Nanofilt | Filtering and trimming of long read sequencing data. | Pathogen characterisation | |
| NanoPlot | NanoPlot is a plotting tool for long read sequencing data and alignments. | Pathogen characterisation | Tool info Training |
| Nanopolish | Software package for signal-level analysis of Oxford Nanopore sequencing data. | Pathogen characterisation | Tool info |
| nanoq | nanoq is an ultra-fast quality control and summary reports for nanopore reads | Pathogen characterisation | Training |
| National Center for Biotechnology Information (NCBI) | The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information. | Human biomolecular data | Training |
| Nextclade | Nextclade is a tool for viral genome clade assignment, mutation calling, and sequence quality checks. | Pathogen characterisation | Tool info Training |
| Nextflow | Nextflow is a framework for data analysis workflow execution | Human biomolecular data Pathogen characterisation | Tool info Training |
| Nextstrain | Nextstrain is an open-source project to harness the scientific and public health potential of pathogen genome data. | Pathogen characterisation | Tool info Standards/Databases Training |
| Nextstrain Auspice | Estonian local instance of the Nextstrain Auspice application that serves SARS-CoV-2 phylogenetic data | SARS-CoV-2 sequencing ... | |
| ngmaster | In silico multi-antigen sequence typing for Neisseria gonorrhoeae (NG-MAST) and Neisseria gonorrhoeae sequence typing for antimicrobial resistance (NG-STAR). | Pathogen characterisation | |
| noWorkFlow | The noWorkflow project aims at allowing scientists to benefit from provenance data analysis even when they don't use a workflow system. | General guidelines | |
| NumPy | Python library for scientific computing. | Socioeconomic data Socioeconomic data | Tool info Training |
| NUTS | The NUTS (Nomenclature of territorial units for statistics) classification, developed by eurostat, is a hierarchical system for dividing up the economic territory of the EU and the UK. | Training | |
| ODDISEI Secure ANalysis Environment (SANE) | SANE is a virtual container in which the researcher can analyse sensitive data, while the data owner retains full control. | Socioeconomic data | |
| OHDSI | The R package will perform data quality checks against an OMOP CDM instance. | Human clinical and hea... | Tool info |
| Omicsgenerator | Omics Integrator is a package designed to integrate proteomic data, gene expression data and/or epigenetic data using a protein-protein interaction network. | Human biomolecular data | |
| OMSSA | OMSSA (Open Mass Spectrometry Search Algorithm) is a tool to identify peptides in tandem mass spectrometry (MS/MS) data. The OMSSA algorithm uses a classic probability score to compute specificity. See also The NCBI C++ Toolkit and The NCBI C++ Toolkit Book. | Pathogen characterisation | Tool info |
| Ontology Lookup Service (OLS) | EMBL-EBI's web portal for finding ontologies | FAIR data Human clinical and hea... | Tool info Standards/Databases Training |
| OpenBEL | The OpenBEL Framework is an open-platform technology for managing, publishing, and using biological knowledge represented using the Biological Expression Language (BEL). | Knowledge Graph Genera... | |
| OpenMS | OpenMS is an open-source software C++ library for LC-MS data management and analyses. | Human biomolecular data Pathogen characterisation | Tool info Training |
| OpenProvenance | Set of user-friendly web applications for storing, validating, and translating W3C PROV-based provenance representations. | General guidelines | |
| OpenRefine | Powerful free, open source tool for working with messy data: cleaning it; transforming it from one format into another; and extending it with web services and external data. | Socioeconomic data | Training |
| outliers | A collection of some tests commonly used for identifying outliers. | Socioeconomic data | Training |
| pandas | Open source data analysis and manipulation tool, built on top of the Python programming language. | Socioeconomic data Socioeconomic data | Tool info Training |
| Pangolin | Pangolin is a tool for the Phylogenetic Assignment of Named Global Outbreak LINeages | Pathogen characterisation | Tool info Training |
| Panther | The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. | Human biomolecular data | Tool info Standards/Databases Training |
| pasty | A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates. | Pathogen characterisation | |
| Pathogens Portal | The Pathogens Portal, launched in July 2023, is an invaluable resource for researchers, clinicians, and policymakers who need access to the latest and most comprehensive datasets on pathogens. The portal is a collaborative effort between the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) and partners. | Pathogen characterisation Linked pathogen and ho... The Swedish Pathogens ... | Standards/Databases Training |
| Pathogens Portal Cohort Browser | The Pathogens Portal Cohort Browser presents discovery metadata of infectious disease cohort datasets and provides links to the associated datasets within ELIXIR Core Data Resources; search and filtering functionalities enable users to identify cohort studies of interest in a convenient manner. | Linked pathogen and ho... | |
| Pathogenwatch | Pathogenwatch provides species and taxonomy prediction for over 60,000 variants of bacteria, viruses, and fungi. | Pathogen characterisation | |
| pbptyper | In silico Penicillin Binding Protein (PBP) typer for Streptococcus pneumoniae assemblies | Pathogen characterisation | |
| PEDDY | Sample quality control. Infer family connections thus revealing any sample mixup during sample collection from families. | Human biomolecular data | |
| PepArMl | A Meta-Search Peptide Identification Platform for Tandem Mass Spectra | Pathogen characterisation | Tool info |
| PHES-ODM | A data model to improve wastewater surveillance through interoperable data. | Pathogen characterisation | |
| PhyML | PhyML is a software package that uses modern statistical approaches to analyse alignments of nucleotide or amino acid sequences in a phylogenetic framework. | Human biomolecular data | Tool info |
| Picard | Picard is a suite of tools that provides quality control and processing of NGS data, including duplicate read removal, format conversion, and alignment. | Pathogen characterisation Human biomolecular data | Tool info |
| PiGx SARS-CoV-2 Wastewater Sequencing Pipeline | PiGx SARS-CoV-2 is a pipeline for analysing data from sequenced wastewater samples and identifying given lineages of SARS-CoV-2. | Pathogen characterisation | |
| Pilon | Pilon is a software tool which can be used to automatically improve draft assemblies and find variation among strains, including large event detection. | Pathogen characterisation | Tool info Training |
| PlasmidID | PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification. | Pathogen characterisation | Tool info |
| Polypolish | Polypolish is a tool for polishing genome assemblies with short reads. | Pathogen characterisation | Tool info Training |
| Population Health Information Research Infrastructure (PHIRI) | PHIRI is the roll-out of the research infrastructure on population health information that aims to facilitate and generate the best available evidence for research on health and well-being of populations as impacted by COVID-19. | Human clinical and hea... | |
| Porechop | Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. | Pathogen characterisation | |
| preseq | The preseq package is aimed at predicting the yield of distinct reads from a genomic library from an initial sequencing experiment. | Pathogen characterisation | Tool info |
| Prokka | Prokka is a software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. | Pathogen characterisation | Tool info Training |
| Prov python | Python implementation of the PROV data model. | General guidelines | Training |
| Provenance storage | A prototype of a provenance management service implementing the CPM (ISO 23494-2). | General guidelines | |
| provR | Collect meta-data from scripts written in the R programming language. | General guidelines | |
| ProvToolbox | Java implementation of the PROV data model. | General guidelines | |
| PyBEL | Pure Python package for parsing and handling biological networks encoded in the Biological Expression Language (BEL). | Knowledge Graph Genera... | Tool info |
| PycoQC | PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data | Pathogen characterisation | Tool info Training |
| pyod | A comprehensive but easy-to-use Python library for detecting anomalies in multivariate data. | Socioeconomic data | |
| QIIME 2 | QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. | Pathogen characterisation | Tool info Training |
| Qualimap | Qualimap is a quality control tool that assesses the quality of the sequencing data at different stages of the analysis pipeline, including read mapping, coverage, and expression analysis. | Pathogen characterisation Human biomolecular data | Tool info Training |
| Quarto | Quarto is an open-source scientific and technical publishing system that enables the creation of dynamic and reproducible content. | Prototyping federated ... | Training |
| Quast | QUAST stands for QUality ASsessment Tool. It evaluates genome/metagenome assemblies by computing various metrics. | Pathogen characterisation | Tool info Training |
| R | Free software environment for statistical computing and graphics. | Tool info Training | |
| R Markdown | R Markdown can help to turn your analyses into high quality documents, reports, presentations and dashboards. | Training | |
| R Shiny | Shiny is an R package that makes it easy to build interactive web apps straight from R. | Training | |
| Racon | Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. | Pathogen characterisation | Tool info Training |
| Raven | Raven is a de novo genome assembler for long uncorrected reads. | Pathogen characterisation | Tool info |
| RAxML | A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies | Pathogen characterisation | Tool info Training |
| RDataTracker | An R library to collect provenance from R scripts. | General guidelines | |
| ReAdW | Convert ThermoFinningan RAW mass spectrometry files to the mzXML format. | Pathogen characterisation | Tool info |
| recordr | Provenance tracking for R | General guidelines | |
| Research Data Centre at the BfArM | Research at the BfArM concentrates on important and contemporary research focal points with regard to the marketing authorisation of medicinal products and improving the safety thereof as well as concerning the recording and assessment of risks in connection with medical devices. | Human clinical and hea... | |
| Research Object Crate (RO-Crate) | RO-Crate is a lightweight approach to packaging research data with their metadata, using schema.org. An RO-Crate is a structured archive of all the items that contributed to the research outcome, including their identifiers, provenance, relations and annotations. | General guidelines | Standards/Databases |
| ResFinder | ResFinder identifies acquired genes and/or finds chromosomal mutations mediating antimicrobial resistance in total or partial DNA sequence of bacteria. | Pathogen characterisation | Tool info |
| RSEM | RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. | Pathogen characterisation | Tool info |
| RSeQC | RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. | Pathogen characterisation | Tool info Training |
| Salmon | Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data | Pathogen characterisation | Tool info Training |
| SAMtools | SAMtools is a suite of programs for interacting with high-throughput sequencing data. | Pathogen characterisation Human biomolecular data Pathogen characterisation | Tool info Training |
| Sapporo WES | Implementation of Workflow Execution Service (WES) or so-called Workflow-as-a-Service. | General guidelines Human clinical and hea... | Tool info |
| SARS-CoV-2 Contextual Data Specification | A SARS-CoV-2 Contextual Data Specification from PHA4GE. | Pathogen characterisation | |
| SARS-CoV-2 Data Hubs | Using technology that builds upon existing EMBL-EBI infrastructure, we provide SARS-CoV-2 Data Hubs to those public health agencies and other scientific groups responsible for generating viral sequence data from the outbreak at national or regional levels. | Human biomolecular data | |
| SARS-COV-2 outbreak in Andalucia | SARS-CoV-2 whole genome sequencing circuit of Andalusia | Human biomolecular data | |
| sccmec | sccmec is a tool for typing SCCmec cassettes in assemblies. | Pathogen characterisation | |
| Schema.org | Schema.org is a collaborative, community activity with a mission to create, maintain, and promote schemas for structured data on the Internet, on web pages, in email messages, and beyond. | Human clinical and hea... General guidelines | Standards/Databases Training |
| Scikit-learn | Machine learning tools in Python | Socioeconomic data Socioeconomic data | Tool info Training |
| SDMX Registry | SDMX Fusion Metadata Registry | Socioeconomic data | |
| SDMX-Reference Infrastructure (SDMX-RI) | The SDMX-Reference Infrastructure (SDMX-RI) is a set of pick-and-choose building blocks and tools that allow data to be exposed to the external world through access rights by using web services. | Socioeconomic data | |
| seaborn | Python data visualization library that provides a high-level interface for drawing attractive and informative statistical graphics. | Socioeconomic data | Training |
| SeqSero2 | Salmonella serotype prediction from genome sequencing data. | Pathogen characterisation | Tool info |
| ShigaTyper | ShigaTyper is a quick and easy tool designed to determine Shigella serotype using Illumina (single or paired-end) or Oxford Nanopore reads with low computation requirement. | Pathogen characterisation | |
| ShigEiFinder | This is a tool that is used to identify differentiate Shigella/EIEC using cluster-specific genes and identify the serotype using O-antigen/H-antigen genes. | Pathogen characterisation | Tool info |
| SICER2 | Redesigned and improved ChIP-seq broad peak calling tool SICER | Human biomolecular data | |
| Singularity | Singularity is a widely-adopted container runtime that implements a unique security model to mitigate privilege escalation risks and provides a platform to capture a complete application environment into a single file (SIF) | Human biomolecular data | Training |
| SISTR | Salmonella serovar predictions from whole-genome sequence assemblies by determination of antigen gene and cgMLST gene alleles using BLAST. | Pathogen characterisation | Tool info |
| Snakemake | Snakemake is a framework for data analysis workflow execution | Human biomolecular data Pathogen characterisation General guidelines Human clinical and hea... | Tool info Training |
| SNippy | Rapid haploid variant calling and core genome alignment. | Pathogen characterisation | Tool info Training |
| SnpEff | Genetic variant annotation and functional effect prediction toolbox. It annotates and predicts the effects of genetic variants on genes and proteins. | Human biomolecular data Pathogen characterisation | Tool info Training |
| SnpSift | SnpSift annotates genomic variants using databases, filters, and manipulates genomic annotated variants. | Pathogen characterisation | Tool info |
| SOAPnuke | A novel analysis tool developed for quality control and preprocessing of FASTQ and SAM/BAM data. | Pathogen characterisation | Tool info |
| SortMeRNA | SortMeRNA is a local sequence alignment tool for filtering, mapping and clustering. | Pathogen characterisation | Tool info Training |
| SPAdes | SPAdes is an assembly toolkit containing various assembly pipelines. | Human biomolecular data Pathogen characterisation | Tool info Training |
| spaTyper | Given a fasta file or multiple fasta files, identifies the repeats and the order and generates a spa type. | Pathogen characterisation | |
| SRA | The SRA is NIH's primary archive of high-throughput sequencing data and is part of the International Nucleotide Sequence Database Collaboration (INSDC) that includes at the NCBI Sequence Read Archive (SRA), the European Bioinformatics Institute (EBI), and the DNA Database of Japan (DDBJ). Data submitted to any of the three organizations are shared among them. SRA accepts data from all kinds of sequencing projects including clinically important studies that involve human subjects or their metagenomes, which may contain human sequences. These data often have a controlled access via dbGaP (the database of Genotypes and Phenotypes). | Human biomolecular data | Tool info Standards/Databases Training |
| SsuisSero | This pipeline is designed to rapidly infer Streptococcus suis serotype from Oxford Nanopore data by first assemblying a draft genome using Flye followed by genome polishing with racon and medaka. | Pathogen characterisation | |
| Stanford HIV Drug Resistance Database (HIVDB) | A curated database containing nearly all published HIV RT and protease sequences: a resource designed for researchers studying evolutionary and drug-related variation in the molecular targets of anti-HIV therapy. | Pathogen characterisation | |
| STAR | Spliced Transcripts Alignment to a Reference | Human biomolecular data Pathogen characterisation | Tool info Training |
| StreamFlow | Container-native workflow manager for hybrid infrastructures | General guidelines Human clinical and hea... | |
| Swedish Pathogens Portal | The Swedish Pathogens Portal was previously known as the Swedish COVID-19 Data Portal. It is the Swedish national node of the Pathogens Portal, aimed at facilitating the sharing of data related to pathogens and pandemic preparedness. | Pathogen characterisation The Swedish Pathogens ... | Standards/Databases |
| TBProfiler | TBProfiler can rapidly and accurately predict anti-TB drug resistance profiles across large numbers of samples with WGS data. | Pathogen characterisation | |
| The Cancer Genome Atlas (TCGA) | The Cancer Genome Atlas (TCGA) is a comprehensive, collaborative effort led by the National Institutes of Health (NIH) to map the genomic changes associated with specific types of tumors to improve the prevention, diagnosis and treatment of cancer. Its mission is to accelerate the understanding of the molecular basis of cancer through the application of genome analysis and characterization technologies. | Human biomolecular data | Standards/Databases Training |
| The Data Use Ontology (DUO) | The Data Use Ontology (DUO) describes data use requirements and limitations. DUO allows to semantically tag datasets with restriction about their usage, making them discoverable automatically based on the authorization level of users, or intended usage. This resource is based on the OBO Foundry principles, and developed using the W3C Web Ontology Language. It is used in production by the European Genome-phenome Archive (EGA) at EMBL-EBI and CRG as well as the Broad Institute for the Data Use Oversight System (DUOS). | FAIR data Human biomolecular data | Standards/Databases |
| The European Health Information Gateway | The European Health Information Gateway is a platform that provides access to various health information resources and datasets from across Europe, including data on health systems, health determinants, and health outcomes. | Human clinical and hea... | |
| The National health service metadata catalogue | Tool to find health data in the metadata catalogue in Portugal. | Human clinical and hea... | |
| The Open Biological and Biomedical Ontology (OBO) Foundry | Collaborative effort to develob interoperable ontologies for the biological sciences | Human clinical and hea... | Standards/Databases |
| The Public Service Data Catalogue | Tool to discover the Data held by the Irish Public Service | Human clinical and hea... | |
| tidyr | Tidy data describes a standard way of storing data that is used wherever possible throughout the [tidyverse](https://www.tidyverse.org/). | Socioeconomic data | |
| toil-cwl-runner | The toil-cwl-runner command provides cwl-parsing functionality using cwltool, and leverages the job-scheduling and batch system support of Toil. | Human biomolecular data | |
| Trifacta | Trifacta is designed for analysts to explore, transform, and enrich raw data into clean and structured formats. | Socioeconomic data | |
| Trimmomatic | Trimmomatic is a tool used for the removal of adapter sequences, low-quality reads, and sequences with ambiguous bases from NGS data. | Pathogen characterisation Human biomolecular data | Tool info Training |
| UCSC Genome Browser | An online tool for analyzing and visualizing genomic data. It allows users to add and share annotations. | Human biomolecular data An automated SARS-CoV-... | Tool info Standards/Databases Training |
| Unicycler | Unicycler is an assembly pipeline for bacterial genomes. For the best possible assemblies, give it both Illumina reads and long reads, and it will conduct a short-read-first hybrid assembly. | Pathogen characterisation | Tool info Training |
| UNottingham Beacon | Beacon from UNottingham to query a backend OMOP database of synthetic COVID-19 patient EHRs (electronic health records). | Human biomolecular data | |
| validate R package | Declare data validation rules and data quality indicators; confront data with them and analyze or visualize the results. | Socioeconomic data | |
| VarScan | Variant calling and somatic mutation/CNV detection for next-generation sequencing data | Human biomolecular data | Tool info Training |
| VCFtools | VCFtools is a program package designed for working with VCF files. | Pathogen characterisation | Tool info |
| Velvet | Velvet is an algorithm package that has been designed to deal with de novo genome assembly and short read sequencing alignments. | Pathogen characterisation | Tool info Training |
| VEP | VEP (Variant Effect Predictor) predicts the functional effects of genomic variants. | Human biomolecular data Pathogen characterisation | Tool info Training |
| Viral AI | A global network for genomic surveillance and infectious disease research | Human biomolecular data | |
| VLQ | A pipeline for lineage abundance estimation from wastewater sequencing data. | Pathogen characterisation | |
| Webin-CLI | Command line application to submit assemblies and transcriptomes to ENA. | Using the ENA data sub... | Training |
| WfExS | Workflow Execution Service Backend (WfExS-backend) is a high-level orchestrator to run scientific workflows reproducibly. | General guidelines | |
| WorkflowHub | A registry for describing, sharing and publishing scientific computational workflows. | Pathogen characterisation An automated SARS-CoV-... | Tool info Standards/Databases Training |
| wtdbg2 | Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). | Human biomolecular data | Tool info |
| X! Tandem | X! Tandem open source is software that can match tandem mass spectra with peptide sequences, in a process that has come to be known as protein identification. | Pathogen characterisation | |
| xcms | Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. | Pathogen characterisation | Tool info Training |
| XCMS Online | A systems biology tool for analyzing metabolomic data. It automatically superimposes raw metabolomic data onto metabolic pathways and integrates it with transcriptomic and proteomic data. | Human biomolecular data | Tool info |
| Zenodo | Zenodo is a generalist research data repository built and developed by OpenAIRE and CERN. | FAIR data Human biomolecular data | Standards/Databases Training |
| Epidemiology of Infectious Diseases (Epistat) | A web based application for visualising and exploring data on infectious diseases monitored by Sciensano. |
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| COVID Epistat | Dashboard for COVID-19 epidemiological data (vaccination, laboratory testing, wastewater, variants, hospitalised patients, mortality, nursing home patients, mental health indicators, seroprevalence). |
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| Sciensano R Shiny Apps | Shiny is an R package that makes it easy to build interactive web apps straight from R. At Sciensano, several Shiny Apps have been developed to process, analyse and visualise data during the COVID-19 crisis. These include the Surge App (monitoring and data quality of COVID-19 hospitalisations), Indicator App (COVID-19 indicators based on test positivity rates per province), Coverage App (coverage of clinical database on hospitalised patients), Hospital Indicators (forecasting and profile of hospitalised patients), and Quality of reporting (quality indicators of reporting by individual hospitals).
R Shiny
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| R Markdown | Tool at Sciensano for generating weekly and daily reports. |
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| Sciensano LimeSurvey | Tool for online surveys.
LimeSurvey
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| DMPonline.be | Tool that provides templates for data management plans. |
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| Figures on notifiable infectious diseases | Dashboard for notifiable infectious diseases in Flanders. |
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| Galaxy Belgium | Galaxy Belgium is a Galaxy instance managed by the Belgian ELIXIR node, funded by the Flemish government, which utilises infrastructure provided by the Flemish Supercomputer Center (VSC).
Galaxy
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| COVID-NL clinical data dashboard | The Dutch national COVID-19 clinical data dashboard allows exploration and reuse of clinical data from Dutch university medical centers (UMCs). The dashboard provides researchers with a clear overview of what is available, allows searching for specific data and makes access to such data easier when the necessary ethical and legal conditions have been met. The policy for access to and sharing of clinical COVID-19 is described in the HRI COVID policy document. |
Standards/Databases | |
| COVID-NL metadata portal | The Dutch national COVID-19 metadata portal describes the content of the collections and type of data. The underlying data remains at the source, but where possible a link to the data or the data request procedure are provided on the portal. The first health care data sets in the portal are coming from observational studies funded by ZonMw, NFU COVID-19 clinical research data, collaborating top clinical hospitals (STZ), as well as other regional hospitals. However, the portal is open to any health care provider wishing to make their COVID-19 data available for research. |
Standards/Databases | |
| ODISSEI | The Open Data Infrastructure for Social Science and Economic Innovations (ODISSEI) is the national research infrastructure for the social sciences in the Netherlands. |
Standards/Databases | |
| DANS Data Station Life Sciences | The Data Archiving and Networked Services (DANS) is the Dutch national centre of expertise and repository for research data. This data station allows you to deposit and search for data within the fields of medical, health and green life sciences. |
Standards/Databases | |
| DANS Data Station Life Sciences | The Data Archiving and Networked Services (DANS) is the Dutch national centre of expertise and repository for research data. This data station allows you to deposit and search for data within the social sciences and humanities. |
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| ELSI servicedesk | The ELSI Servicedesk provides guidance and answers to the ethical, legal and social implications of research on personalised medicine and next generation sequencing that life science professionals, policymakers and patients are faced with. |
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| SARS-CoV-2 Database | Norwegian SARS-CoV-2 database |
Standards/Databases | |
| Folkehelseinstituttet (FHI) | Norwegian Institute of Public Health (NIPH) portal for infectious disease information |
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| FEGA Norway | Federated European Genome-phenome Archive (EGA) node
European Genome-phenome Archive (EGA)
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| Swedish Pathogens Portal | The Swedish Pathogens Portal is a hub for data, tools, services, and other resources centred around pathogens, such as SARS-CoV-2, and pandemic preparedness in Sweden. |
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| Swiss Pathogen Surveillance Platform (SPSP) | SPSP is a secure One-health online platform that enables near real-time sharing under controlled access of pathogen genomic data and their associated clinical/epidemiological metadata. During COVID-19, it served as the Swiss SARS-CoV-2 genomic data hub, collecting data, annotating it, communicating reports to the federal public health authorities and openly re-sharing anonymised data on the Covid-19 Data Platform. |
Pathogen characterisation Pathogen characterisation Pathogen characterisation | |
| Research Data Management (RDM) sources in Switzerland | RDMkit page on Switzerland’s RDM guidelines and resources. |
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| COVID-19 Data Portal aggregation of Swiss COVID-19 data | COVID-19 Data Portal aggregation of Swiss COVID-19 data |
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| V-pipe | V-pipe is the bioinformatics pipeline that integrates various open-source software packages for assessing viral genetic diversity from next-generation sequencing (NGS) data derived from intra-host virus populations |
Pathogen characterisation | |
| ViralZone | ViralZone is a SIB Swiss Institute of Bioinformatics web-resource for all viral genus and families, providing general molecular and epidemiological information, along with virion and genome figures. Each virus or family page gives an easy access to UniProtKB/Swiss-Prot viral protein entries |
Pathogen characterisation | |
| Nextstrain | Nextstrain is an open-source project to harness the scientific and public health potential of pathogen genome data. It provides a continually-updated view of publicly available data alongside powerful analytic and visualization tools for use by the community. The goal is to aid epidemiological understanding and improve outbreak response |
Pathogen characterisation | |
| CoV Spectrum | CoV-Spectrum is an interactive tool to analyze and discover variants of SARS-CoV-2. Main features include a powerful search engine that supports amino acid and nucleotide mutation filtering, the comparison of multiple variants, and a built-in fitness advantage estimation model. |
Pathogen characterisation | |
| Covariants | CoVariants provides an overview of SARS-CoV-2 variants and mutations that are of interest. It displays what mutations define a variant, what impact they might have (with links to papers and resources), where variants are found, and link the variants in Nextstrain. |
Pathogen characterisation | |
| COVTriage | COVTriage is a search engine developed as part of SIBiLS (Swiss Institute of Bioinformatics Literature Services), which purpose is to rank the COVID-19 literature (Medline, PMC, Cord-19) according to the 9 axes of the COVoc ontology (controlled vocabulary to support literature triage for COVID-19). This resource supports COVID-19 / SARS-CoV-2 research. |
Pathogen characterisation | |
| Computational Linguistics for COVID-19 | To process COVID-19-related scientific publications automatically to detect mentions of domain-specific entities of particular relevance (such as genes, symptoms, drugs, organs, etc.). To enhance accessibility to the literature, for example, simplifying the search of papers dealing with a particular gene or identifying unexpected connections between different entities. |
Pathogen characterisation |