Dataset Information

EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts.

ABSTRACT:

Summary

Genomics 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.

SUBMITTER: Lo CC

PROVIDER: S-EPMC9113274 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature

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Publications

EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts.

Lo Chien-Chi CC Shakya Migun M Connor Ryan R Davenport Karen K Flynn Mark M Gutiérrez Adán Myers Y AMY Hu Bin B Li Po-E PE Jackson Elais Player EP Xu Yan Y Chain Patrick S G PSG

Bioinformatics (Oxford, England) 20220501 10

<h4>Summary</h4>Genomics 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 criti ...[more]

PMID: 35561186

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Project description:BackgroundThe improvements in genomics methods coupled with readily accessible high-throughput sequencing have contributed to our understanding of microbial species, metagenomes, infectious diseases and more. To maximize the impact of these genomics studies, it is important that data from biological samples will become publicly available with standardized metadata. The availability of data at public archives provides the hope that greater insights could be obtained through integration with multi-omics data, reproducibility of published studies, or meta-analyses of large diverse datasets. These datasets should include a description of the host, organism, environmental source of the specimen, spatial-temporal information and other relevant metadata, but unfortunately these attributes are often missing and when present, they show inconsistencies in the use of metadata standards and ontologies.ResultsMETAGENOTE ( https://metagenote.niaid.nih.gov ) is a web portal that greatly facilitates the annotation of samples from genomic studies and streamlines the submission process of sequencing files and metadata to the Sequence Read Archive (SRA) (Leinonen R, et al, Nucleic Acids Res, 39:D19-21, 2011) for public access. This platform offers a wide selection of packages for different types of biological and experimental studies with a special emphasis on the standardization of metadata reporting. These packages follow the guidelines from the MIxS standards developed by the Genomics Standard Consortium (GSC) and adopted by the three partners of the International Nucleotides Sequencing Database Collaboration (INSDC) (Cochrane G, et al, Nucleic Acids Res, 44:D48-50, 2016) - National Center for Biotechnology Information (NCBI), European Bioinformatics Institute (EBI) and the DNA Data Bank of Japan (DDBJ). METAGENOTE then compiles, validates and manages the submission through an easy-to-use web interface minimizing submission errors and eliminating the need for submitting sequencing files via a separate file transfer mechanism.ConclusionsMETAGENOTE is a public resource that focuses on simplifying the annotation and submission process of data with its corresponding metadata. Users of METAGENOTE will benefit from the easy to use annotation interface but most importantly will be encouraged to publish metadata following standards and ontologies that make the public data available for reuse.

Dataset Information

EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts.

Summary

Availability and implementation

Supplementary information

Publications

EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts.

Similar Datasets

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