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ReCo:单个和组合CRISPR gRNA的自动NGS读数计数

Martin Wegner¹, Manuel Kaulich^1,2,3

¹Goethe University Frankfurt, University Hospital, Institute of Biochemistry II, 60590, Frankfurt am Main, Germany.

Bioinformatics (Oxford, England)

|July 23, 2023

概括

研究人员开发了ReCo,这是一款简单易用的工具,简化了CRISPR屏幕分析. 该软件自动化了下一代测序数据的转化为读数表,有助于基因型-表型关联研究.

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.
分子生物学分子生物学

背景情况:

克里斯普尔屏对于将基因型与表型联系起来至关重要.
从这些屏幕上分析高通量下一代测序 (NGS) 数据传统上需要专门的计算专业知识.
现有的方法在下游分析之前需要复杂的数据转换步骤.

研究的目的:

开发一个用户友好的,独立的工具来分析CRISPR屏幕NGS数据.
从单个和组合CRISPR库自动生成读数表.
为了简化指导RNA (gRNA) 诱导的表型的识别.

主要方法:

开发了ReCo,这是一个集成cutadapt和bowtie2的软件工具.
实现了NGS读数的自动序列修剪和对齐.
设计ReCo以从分阶段NGS数据生成读数表.

主要成果:

ReCo成功地自动生成了CRISPR屏幕数据的读数表.
该工具简化了转换原始NGS数据的过程.
能够进行高效的下游分析来识别gRNA诱导的表型.

结论:

ReCo显著降低了CRISPR屏幕分析的计算障碍.
该工具通过简化数据处理来促进基因型-表型关联研究.
ReCo提高了CRISPR查方法的可访问性和效率.

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相关概念视频

CRISPR and crRNAs

CRISPR and crRNAs

Bacteria and archaea are susceptible to viral infections just like eukaryotes; therefore, they have developed a unique adaptive immune system to protect themselves. Clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) are present in more than 45% of known bacteria and 90% of known archaea.
The CRISPR-Cas system stores a copy of foreign DNA in the host genome and uses it to identify the foreign DNA upon reinfection. CRISPR-Cas has three different...