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拉皮斯是一个快速的网络API,用于大规模的开放病毒测序数据

Chaoran Chen^1,2, Alexander Taepper^3,4, Fabian Engelniederhammer⁵

¹Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland. chaoran.chen@bsse.ethz.ch.

BMC bioinformatics

|June 5, 2023

概括

基因组测序数据对于追踪病原体传播至关重要. 序列轻量级API (LAPIS) 为基因组流行病学提供了快速,高效的访问和分析这些重要数据.

科学领域:

基因组学就是基因组学.
生物信息学是一种生物信息学.
流行病学流行病学

背景情况:

基因组测序数据对于跟踪SARS-CoV-2和mopox等传染病爆发至关重要.
快速生成序列数据需要高效的访问和处理工具.

研究的目的:

开发一个快速检索和分析大规模基因组测序数据的系统.
为应对大量病原体序列数据的访问和处理所面临的挑战.

主要方法:

开发了一个简单的序列API (LAPIS),一个REST API.
使用了一种新的内存数据库引擎来实现高速数据处理.
实现了对突变和元数据的复杂查询功能.

主要成果:

拉皮斯展示了高速和吞吐量,处理了超过2000万个请求,对于1450万个SARS-CoV-2序列的毫秒响应时间.
该系统支持基于突变和元数据的复杂查询和数据聚合.
拉皮斯作为公共仪表板追踪SARS-CoV-2和mopox的后端.

结论:

通过优化的数据库和Web API,LAPIS提高了基因组数据的可访问性.
它被设计为用于仪表板和分析的多功能后端.
与GenBank等主要数据库集成的潜力存在.

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