CRISPR-DAV：CRISPR NGS 数据分析和可视化流程。

CRISPR-DAV: CRISPR NGS data analysis and visualization pipeline.

机构信息

Translational Bioinformatics & Computational Genomics.

Leads Discovery & Optimization.

出版信息

Bioinformatics. 2017 Dec 1;33(23):3811-3812. doi: 10.1093/bioinformatics/btx518.

DOI:10.1093/bioinformatics/btx518

PMID:28961906

Abstract

SUMMARY

The simplicity and precision of CRISPR/Cas9 system has brought in a new era of gene editing. Screening for desired clones with CRISPR-mediated genomic edits in a large number of samples is made possible by next generation sequencing (NGS) due to its multiplexing. Here we present CRISPR-DAV (CRISPR Data Analysis and Visualization) pipeline to analyze the CRISPR NGS data in a high throughput manner. In the pipeline, Burrows-Wheeler Aligner and Assembly Based ReAlignment are used for small and large indel detection, and results are presented in a comprehensive set of charts and interactive alignment view.

AVAILABILITY AND IMPLEMENTATION

CRISPR-DAV is available at GitHub and Docker Hub repositories: https://github.com/pinetree1/crispr-dav.git and https://hub.docker.com/r/pinetree1/crispr-dav/.

CONTACT

xuning.wang@bms.com.

摘要

CRISPR/Cas9 系统的简洁性和精确性带来了基因编辑的新时代。由于其多重性，下一代测序（NGS）使得对大量样本中具有所需基因组编辑的期望克隆进行筛选成为可能。在这里，我们提出了 CRISPR-DAV（CRISPR 数据分析和可视化）管道，以高通量的方式分析 CRISPR NGS 数据。在该管道中，使用 Burrows-Wheeler 对齐器和基于组装的重对齐来检测小和大的插入缺失，并以一套全面的图表和交互式对齐视图呈现结果。