A user-friendly and sequencing platform-independent bioinformatics pipeline to build SARS-CoV-2 complete genomes from raw sequencing reads and to investigate variants.
The pipeline is implemented as a Galaxy (https://galaxyproject.org/) workflow integrated with a personalised IRIDA (https://www.irida.ca/) instance.
The file Galaxy-Workflow-SARS-CoV-2_RECoVERY_4.0.ga contains the Galaxy workflow that can be imported into any Galaxy instance.
The tools directory contains some personalised tools that the pipeline uses. All other tools can be installed directly from the Galaxy Toolshed.
A preprint is available at: https://doi.org/10.1101/2021.01.16.425365
