CRISPR-DAV: CRISPR NGS data analysis and visualization pipeline

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

Authors

Xuning Wang¹, Charles Tilford¹, Isaac Neuhaus¹, Gabe Mintier², Qi Guo³, John N Feder², Stefan Kirov¹

Affiliations

¹ Translational Bioinformatics & Computational Genomics.
² Leads Discovery & Optimization.
³ Genome Biology, Bristol-Myers Squibb Co., Pennington, NJ 08534, USA.

PMID: 28961906
DOI: 10.1093/bioinformatics/btx518

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.

MeSH terms

Bacteria / genetics
Clone Cells*
Clustered Regularly Interspaced Short Palindromic Repeats*
Genome, Bacterial
Genomics / methods
High-Throughput Nucleotide Sequencing / methods*
INDEL Mutation*
Sequence Analysis, DNA / methods*
Software*