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

• Published in: arXiv.org 2021-06
• Main Authors: Chien-Chi Lo, Shakya, Migun, Davenport, Karen, Flynn, Mark, Adán Myers y Gutiérrez, Hu, Bin, Po-E Li, Elais Player Jackson, Xu, Yan, Chain, Patrick S G
• Format: Article
• Language: English
• Subjects: Applications programs; Coronaviruses; COVID-19; Decision analysis; Epidemiology; Gene sequencing; Genomes; Infectious diseases; Outbreaks; Porosity; Severe acute respiratory syndrome coronavirus 2; Source code; Viral diseases
• ISSN: 2331-8422

Genomics has become an essential technology for surveilling emerging infectious disease outbreaks. A wide range of technologies and strategies for pathogen genome enrichment and sequencing are being used by laboratories worldwide, together with different, and sometimes ad hoc, analytical procedures for generating genome sequences. As a result, public repositories now contain non-standard entries of varying quality. A standardized analytical process for consensus genome sequence determination, particularly for outbreaks such as the ongoing COVID-19 pandemic, is critical to provide a solid genomic basis for epidemiological analyses and well-informed decision making. To address this need, we have developed a bioinformatic workflow to standardize the analysis of SARS-CoV-2 sequencing data generated with either the Illumina or Oxford Nanopore platforms. Using an intuitive web-based interface, this workflow automates SARS-CoV-2 reference-based genome assembly, variant calling, lineage determination, and provides the ability to submit the consensus sequence and necessary metadata to GenBank or GISAID. Given a raw Illumina or Oxford Nanopore FASTQ read file, this web-based platform enables non-bioinformatics experts to automatically produce a SARS-CoV-2 genome that is ready for submission to GISAID or GenBank. Availability:https://edge-covid19.edgebioinformatics.org;https://github.com/LANL-Bioinformatics/EDGE/tree/SARS-CoV2