About: 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 https://covid19.edgebioinformatics.org, and as a Docker container at https://hub.docker.com/r/bioedge/edge-covid19 for local installation.   Goto Sponge  NotDistinct  Permalink

An Entity of Type : fabio:Abstract, within Data Space : covidontheweb.inria.fr associated with source document(s)

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  • 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 https://covid19.edgebioinformatics.org, and as a Docker container at https://hub.docker.com/r/bioedge/edge-covid19 for local installation.
Subject
  • Software architecture
  • Concepts in ethics
  • 2019 disasters in China
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