An online coronavirus analysis platform from the National Genomics Data Center

Zool Res. 2020 Nov 18;41(6):705-708. doi: 10.24272/j.issn.2095-8137.2020.065.

Abstract

Since the first reported severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in December 2019, coronavirus disease 2019 (COVID-19) has become a global pandemic, spreading to more than 200 countries and regions worldwide. With continued research progress and virus detection, SARS-CoV-2 genomes and sequencing data have been reported and accumulated at an unprecedented rate. To meet the need for fast analysis of these genome sequences, the National Genomics Data Center (NGDC) of the China National Center for Bioinformation (CNCB) has established an online coronavirus analysis platform, which includes de novoassembly, BLAST alignment, genome annotation, variant identification, and variant annotation modules. The online analysis platform can be freely accessed at the 2019 Novel Coronavirus Resource (2019nCoVR) (https://bigd.big.ac.cn/ncov/online/tools).

自2019年12月新型冠状病毒(SARS-COV-2)爆发以来,新冠肺炎疫情已扩散至全球大部分国家和地区。随着世界各国对新冠病毒检测和研究工作的开展,冠状病毒基因组序列和测序数据以前所未有的速度产出和积累。为了给科研人员提供高效、便捷、免费的新冠病毒基因组数据分析服务,以满足快速增长的新冠病毒基因组数据分析需求,国家生物信息中心(CNCB)/国家基因组科学数据中心(NGDC)建立了冠状病毒在线分析平台(https://bigd.big.ac.cn/ncov/online/tools),用户无需注册或登录便可直接使用。该平台由基因组拼接、BLAST比对、基因组注释、变异鉴定和变异注释五个模块组成。其中,基因组拼接模块可用于组装二代测序数据;BLAST比对模块可提供与SARS-CoV-2参考基因组、2019 新型冠状病毒信息库(2019nCoVR)、冠状病毒基因组数据库的序列比较;基因组注释模块可识别病毒编码序列和蛋白质序列,并生成GenBank格式注释文件;变异鉴定模块可分别从完整基因组序列或长片段、二代高通量测序数据中检测变异位点;变异注释模块可以分析变异位点所在基因、密码子和氨基酸的改变,评估对基因功能影响的程度。下一步,我们将广泛收集研究人员的分析需求和建议,集成更多专业化的冠状病毒数据分析工具,不断优化分析流程和运行参数,为研究人员提供持续稳定、方便易用的数据分析服务。.

Keywords: Coronavirus; Genome annotation; High-throughput sequencing; Variant identification; de novo assembly.

Publication types

  • Letter
  • Multicenter Study

MeSH terms

  • Animals
  • Betacoronavirus / classification
  • Betacoronavirus / genetics*
  • Betacoronavirus / physiology
  • COVID-19
  • China
  • Computational Biology / methods*
  • Computational Biology / organization & administration
  • Coronavirus Infections / diagnosis*
  • Coronavirus Infections / virology
  • Genetic Variation
  • Genome, Viral / genetics*
  • Genomics / methods*
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Internet
  • Molecular Sequence Annotation
  • Pandemics
  • Pneumonia, Viral / diagnosis*
  • Pneumonia, Viral / virology
  • SARS-CoV-2

Grant support

This work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB38030200,XDB38050300, XDA19090116, XDA19050302) and National Key R&D Program of China (2020YFC0848900, 2020YFC0847000)