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SARS-CoV-2 RECoVERY: a multi-platform open-source bioinformatic pipeline for the automatic construction and analysis of SARS-CoV-2 genomes from NGS sequencing data
bioRxiv - Bioinformatics Pub Date : 2021-02-05 , DOI: 10.1101/2021.01.16.425365
Luca De Sabato , Gabriele Vaccari , Arnold Knijn , Giovanni Ianiro , Ilaria Di Bartolo , Stefano Morabito

Background: Since its first appearance in December 2019, the novel Severe Acute Respiratory Syndrome Coronavirus type 2 (SARSCoV2), spread worldwide causing an increasing number of cases and deaths (35,537,491 and 1,042,798, respectively at the time of writing, https://covid19.who.int). Similarly, the number of complete viral genome sequences produced by Next Generation Sequencing (NGS), increased exponentially. NGS enables a rapid accumulation of a large number of sequences. However, bioinformatics analyses are critical and require combined approaches for data analysis, which can be challenging for non bioinformaticians. Results: A user friendly and sequencing platform-independent bioinformatics pipeline, named SARSCoV2 RECoVERY (REconstruction of CoronaVirus gEnomes & Rapid analYsis) has been developed to build SARSCoV2 complete genomes from raw sequencing reads and to investigate variants. The genomes built by SARSCoV2 RECoVERY were compared with those obtained using other software available and revealed comparable or better performances of SARSCoV2 RECoVERY. Depending on the number of reads, the complete genome reconstruction and variants analysis can be achieved in less than one hour. The pipeline was implemented in the multi usage open source Galaxy platform allowing an easy access to the software and providing computational and storage resources to the community. Conclusions: SARSCoV2 RECoVERY is a piece of software destined to the scientific community working on SARSCoV2 phylogeny and molecular characterisation, providing a performant tool for the complete reconstruction and variants analysis of the viral genome. Additionally, the simple software interface and the ability to use it through a Galaxy instance without the need to implement computing and storage infrastructures, make SARSCoV2 RECoVERY a resource also for virologists with little or no bioinformatics skills. Availability and implementation: The pipeline SARSCoV2 RECoVERY (REconstruction of COronaVirus gEnomes & Rapid analYsis) is implemented in the Galaxy instance ARIES (https://aries.iss.it).

中文翻译:

SARS-CoV-2 RECoVERY:一种多平台开源生物信息学管道,用于根据NGS测序数据自动构建和分析SARS-CoV-2基因组

背景:自2019年12月首次出现以来,新型2型严重急性呼吸系统综合症冠状病毒(SARSCoV2)遍及全球,导致病例和死亡人数增加(撰写本文时分别为35,537,491和1,042,798),https:// covid19 .who.int)。同样,下一代测序(NGS)产生的完整病毒基因组序列的数量呈指数增长。NGS可以快速积累大量序列。但是,生物信息学分析至关重要,需要采用组合方法进行数据分析,这对非生物信息学专家可能具有挑战性。结果:名为SARSCoV2 RECoVERY(冠状病毒gEnomes和 已经开发了快速分析法以从原始测序读数构建SARSCoV2完整基因组并研究变体。将SARSCoV2 RECoVERY构建的基因组与使用其他可用软件获得的基因组进行比较,并揭示出SARSCoV2 RECoVERY的性能相当或更好。根据读取次数,可以在不到一小时的时间内完成完整的基因组重建和变异分析。该管道在多用途开源Galaxy平台中实现,可以轻松访问该软件并为社区提供计算和存储资源。结论:SARSCoV2 RECoVERY是一款发往科学界的软件,致力于SARSCoV2的系统发育和分子鉴定,为病毒基因组的完整重建和变异分析提供了高性能工具。此外,简单的软件界面以及通过Galaxy实例使用它的能力,而无需实现计算和存储基础架构,使SARSCoV2 RECoVERY成为几乎没有生物信息学技能或没有生物信息学技能的病毒学家的资源。可用性和实施​​:管道SARSCoV2 RECoVERY(冠状病毒gEnomes的重建和快速分析)在Galaxy实例ARIES(https://aries.iss.it)中实现。
更新日期:2021-02-07
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