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.
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.
Authors: Kendell Clement; Holly Rees; Matthew C Canver; Jason M Gehrke; Rick Farouni; Jonathan Y Hsu; Mitchel A Cole; David R Liu; J Keith Joung; Daniel E Bauer; Luca Pinello Journal: Nat Biotechnol Date: 2019-03 Impact factor: 54.908
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Authors: Beau R Webber; Cara-Lin Lonetree; Mitchell G Kluesner; Matthew J Johnson; Emily J Pomeroy; Miechaleen D Diers; Walker S Lahr; Garrett M Draper; Nicholas J Slipek; Branden A Smeester; Klaus N Lovendahl; Amber N McElroy; Wendy R Gordon; Mark J Osborn; Branden S Moriarity Journal: Nat Commun Date: 2019-11-19 Impact factor: 14.919
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