EDGE COVID-19: A Web Platform to generate submission-ready genomes for SARS-CoV-2 sequencing efforts
Chien-Chi Lo, Migun Shakya, Karen Davenport, Mark Flynn, Ad\'an Myers, y Guti\'errez, Bin Hu, Po-E Li, Elais Player Jackson, Yan Xu, Patrick S. G., Chain
TL;DR
EDGE COVID-19 is a user-friendly web platform that standardizes SARS-CoV-2 genome analysis from raw sequencing data, enabling non-experts to generate submission-ready genomes for public repositories.
Contribution
It introduces an automated, web-based workflow for SARS-CoV-2 genome assembly and submission, simplifying processes for non-bioinformatics users during the COVID-19 pandemic.
Findings
Automates genome assembly and variant calling from raw data.
Enables direct submission to GISAID and GenBank.
Supports Illumina and Oxford Nanopore sequencing platforms.
Abstract
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…
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Taxonomy
TopicsGenomics and Phylogenetic Studies · Bacteriophages and microbial interactions · Microbial infections and disease research