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

Authors :: Wang X
Tilford C
Neuhaus I
Mintier G
Guo Q
Feder JN
Kirov S
Source :: Bioinformatics (Oxford, England) [Bioinformatics] 2017 Dec 01; Vol. 33 (23), pp. 3811-3812.
Publication Year :: 2017
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.<br />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/.<br />Contact: xuning.wang@bms.com.<br /> (© The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com)