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 | 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 | 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 |
| 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. |