EDGE COVID-19: A Web Platform to generate submission-ready genomes for SARS-CoV-2 sequencing efforts

Genomics has become a pivotal technology for understanding emerging outbreaks of infectious diseases. A wide range of technologies and strategies for pathogen genome enrichment and sequencing are being used by laboratories and institutes, resulting in different analytical procedures for generating genome sequences and resulting in non-standard entries of varying quality into public repositories. A standardized analytical process for genome sequence generation, particularly for outbreaks such as the ongoing COVID-19 pandemic, are critical to provide scientists with a solid genomic basis for epidemiology analyses and for making well-informed decisions. To address this challenge, we have developed a web platform (EDGE COVID-19) to run standardized workflows for reference-based genome assembly and to perform further analysis of Illumina or Oxford Nanopore Technologies data for SARS-CoV-2 genome sequencing projects. Given a raw Illumina or Oxford Nanopore FASTQ read file, this web platform automates the production of a SARS-CoV-2 genome that is ready for submission to GISAID or GenBank. EDGE COVID-19 is open-source software that is available as a web application for public use at this https URL, and as a Docker container at this https URL for local installation.