论文标题
Edge Covid-19：一个网络平台，用于生成用于SARS-COV-2测序工作的提交准备基因组
EDGE COVID-19: A Web Platform to generate submission-ready genomes for SARS-CoV-2 sequencing efforts
论文作者
论文摘要
基因组学已成为监视新兴的传染病暴发的重要技术。全球实验室正在使用多种病原体基因组富集和测序的技术和策略，以及不同的，有时甚至是临时的分析程序来生成基因组序列。结果，公共存储库现在包含不同质量的非标准条目。共有基因组序列确定的标准化分析过程，特别是对于诸如持续的Covid-19大流行等爆发的疫情，对于为流行病学分析和良好信息做出做出的扎实基因组基础至关重要。为了满足这一需求，我们开发了生物信息学工作流程，以标准化使用Illumina或Oxford Nanobore平台生成的SARS-COV-2测序数据分析。使用基于直观的Web接口，此工作流使基于SARS-COV-2参考的基因组组件，变体调用，谱系确定自动化，并提供了将共识序列和必要元数据提交给GenBank或Gisaid的能力。鉴于RAW Illumina或Oxford Nanopore fastQ读取文件，该基于Web的平台使非生物信息学专家可以自动生产一个可以提交给Gisaid或GenBank的SARS-COV-2基因组。 可用性：https：//esge-covid19.gebioinformatics.org; https：//github.com/lanl-bioinformatics/EDGE/TREE/SARS-COV2
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
