ArticleBioinformatics (Oxford, England)2022
EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts.
Article in Bioinformatics (Oxford, England), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- An evaluation of computational methods for reconstruction of human viral DNA genomes.GigaScience · 2026Article
- A tale of SARS-CoV-2 genomic surveillance in Mali: Variants introductions and transmission dynamics.PloS one · 2026Article
- Methods for safely sharing dual-use genetic data.Frontiers in microbiology · 2026Article
- Sequencing and analysis of 131 SARS-CoV-2 isolates in previously sampled and unsampled regions of Jordan from 2020 to 2023.PloS one · 2025Article
- A cost and community perspective on the barriers to microbiome data reuse.Frontiers in bioinformatics · 2025Article
- Standardized and accessible multi-omics bioinformatics workflows through the NMDC EDGE resource.Computational and structural biotechnology journal · 2024Article
- Article
- Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows.Viruses · 2024Article
- Article
- Nanopore sequencing technology and its applications.MedComm · 2023Review
- Genomic surveillance of severe acute respiratory syndrome coronavirus 2 in Burundi, from May 2021 to January 2022.BMC genomics · 2023Article
- Applying the digital data and the bioinformatics tools in SARS-CoV-2 research.Computational and structural biotechnology journal · 2023Review
- Sierra SARS-CoV-2 sequence and antiviral resistance analysis program.Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology · 2022Article
- Factors affecting SARS-CoV-2 variant distribution in military hospitals in Jordan.Diagnostic microbiology and infectious disease · 2022Article
- SARS-CoV-2 Variants Identification: Overview of Molecular Existing Methods.Pathogens (Basel, Switzerland) · 2022Review
- Molecular Epidemiology of SARS-CoV-2 in Tunisia (North Africa) through Several Successive Waves of COVID-19.Viruses · 2022Article
- A review on viral data sources and search systems for perspective mitigation of COVID-19.Briefings in bioinformatics · 2021Review
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
summaryGenomics has become an essential technology for surveilling emerging infectious disease outbreaks. A 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. A fully integrated analytical process for raw sequence to consensus genome determination, suited to outbreaks such as the ongoing COVID-19 pandemic, is critical to provide a solid genomic basis for epidemiological analyses and well-informed decision making. We have developed a web-based platform and integrated bioinformatic workflows that help to provide consistent high-quality analysis of SARS-CoV-2 sequencing data generated with either the Illumina or Oxford Nanopore Technologies (ONT). Using an intuitive web-based interface, this workflow automates data quality control, SARS-CoV-2 reference-based genome variant and consensus calling, lineage determination and provides the ability to submit the consensus sequence and necessary metadata to GenBank, GISAID and INSDC raw data repositories. We tested workflow usability using real world data and validated the accuracy of variant and lineage analysis using several test datasets, and further performed detailed comparisons with results from the COVID-19 Galaxy Project workflow. Our analyses indicate that EC-19 workflows generate high-quality SARS-CoV-2 genomes. Finally, we share a perspective on patterns and impact observed with Illumina versus ONT technologies on workflow congruence and differences. AVAILABILITY AND IMPLEMENTATION: https://edge-covid19.edgebioinformatics.org, and https://github.com/LANL-Bioinformatics/EDGE/tree/SARS-CoV2. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.