Tools and resources list
| Tool or resource | Description | Related pages | Registry |
|---|---|---|---|
| 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. | Provenance An automated SARS-CoV-2 genome surveillance system built around Galaxy SARS-CoV-2 sequencing in Estonia 2021-2022 | Tool info Training |
| Common Workflow Language (CWL) | An open standard for describing workflows that are build from command line tools | Provenance | Standards/Databases Training |
| Snakemake | Snakemake is a framework for data analysis workflow execution | Provenance | Tool info Training |
| StreamFlow | Container-native workflow manager for hybrid infrastructures | Provenance | |
| Sapporo WES | Implementation of Workflow Execution Service (WES) or so-called Workflow-as-a-Service. | Provenance | Tool info |
| 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. | Provenance | Tool info |
| R Shiny | Shiny is an R package that makes it easy to build interactive web apps straight from R. | Training | |
| R Markdown | R Markdown can help to turn your analyses into high quality documents, reports, presentations and dashboards. | Training | |
| LimeSurvey | LimeSurvey is a free and open source advanced online survey system to create online surveys. | ||
| DMP Online | DMP online is an online planning tool to help you write an effective DMP based on an institutional or funder template. | Training | |
| WorkflowHub | A registry for describing, sharing and publishing scientific computational workflows. | An automated SARS-CoV-2 genome surveillance system built around Galaxy | Tool info Standards/Databases Training |
| CRG COVID-19 Viral Beacon | A platform allowing for browsing SARS-CoV-2 variability at the genome, amino acid, structural, and motif levels | An automated SARS-CoV-2 genome surveillance system built around Galaxy | |
| Galaxy Europe | The European Galaxy server. Provides access to thousands of tools for scalable and reproducible analysis. | An automated SARS-CoV-2 genome surveillance system built around Galaxy | |
| European Nucleotide Archive (ENA) | Provides a record of the nucleotide sequencing information. It includes raw sequencing data, sequence assembly information and functional annotation. | An automated SARS-CoV-2 genome surveillance system built around Galaxy SARS-CoV-2 sequencing in Estonia 2021-2022 | Tool info Standards/Databases Training |
| UCSC Genome Browser | An online tool for analyzing and visualizing genomic data. It allows users to add and share annotations. | An automated SARS-CoV-2 genome surveillance system built around Galaxy | Tool info Standards/Databases |
| 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 in Estonia 2021-2022 | |
| Estonian COVID-19 Data Portal | Estonian instance of the COVID-19 Data Portal. Among other informaiton, served Estonian SARS-CoV-2 sequencing dashboards. | SARS-CoV-2 sequencing in Estonia 2021-2022 | |
| Nextstrain Auspiece | Estonian local instance of the Nextstrain Auspiece application that serves SARS-CoV-2 phylogenetic data | SARS-CoV-2 sequencing in Estonia 2021-2022 | |
| Metagen-FastQC | Cleans metagenomic reads to remove adapters, low-quality bases and host (e.g. human) contamination. | SARS-CoV-2 sequencing in Estonia 2021-2022 | |
| ENA upload tool | Submits experimental data and respective metadata to the European Nucleotide Archive (ENA). | SARS-CoV-2 sequencing in Estonia 2021-2022 | |
| 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.
DMP online
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| Figures on notifiable infectious diseases | Dashboard for notifiable infectious diseases in Flanders. |
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| Galaxy Belgium | Belgian Galaxy instance.
Galaxy
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| ELIXIR Belgium ENA upload tool | Belgium Galaxy instance
Galaxy
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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
The European Genome-phenome Archive (EGA)
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| COVID-19 & Pandemic Preparedness Data Portal Sweden | The Swedish COVID-19 & Pandemic Preparedness Data Portal is a hub for data, tools, services, and other resources centred around COVID-19 and pandemic preparedness in Sweden. |