1. CRISPR-DAV: CRISPR NGS data analysis and visualization pipeline.
- Author
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Wang X, Tilford C, Neuhaus I, Mintier G, Guo Q, Feder JN, and Kirov S
- Subjects
- Bacteria genetics, Genome, Bacterial, Genomics methods, Clone Cells, Clustered Regularly Interspaced Short Palindromic Repeats, High-Throughput Nucleotide Sequencing methods, INDEL Mutation, Sequence Analysis, DNA methods, Software
- 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., (© The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com)
- Published
- 2017
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