CRISPR-DAV: CRISPR NGS data analysis and visualization pipeline - PubMed (original) (raw)
CRISPR-DAV: CRISPR NGS data analysis and visualization pipeline
Xuning Wang et al. Bioinformatics. 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.
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
Similar articles
- BATCH-GE: Batch analysis of Next-Generation Sequencing data for genome editing assessment.
Boel A, Steyaert W, De Rocker N, Menten B, Callewaert B, De Paepe A, Coucke P, Willaert A. Boel A, et al. Sci Rep. 2016 Jul 27;6:30330. doi: 10.1038/srep30330. Sci Rep. 2016. PMID: 27461955 Free PMC article. - CRISPRMatch: An Automatic Calculation and Visualization Tool for High-throughput CRISPR Genome-editing Data Analysis.
You Q, Zhong Z, Ren Q, Hassan F, Zhang Y, Zhang T. You Q, et al. Int J Biol Sci. 2018 May 22;14(8):858-862. doi: 10.7150/ijbs.24581. eCollection 2018. Int J Biol Sci. 2018. PMID: 29989077 Free PMC article. - ReCo: automated NGS read-counting of single and combinatorial CRISPR gRNAs.
Wegner M, Kaulich M. Wegner M, et al. Bioinformatics. 2023 Aug 1;39(8):btad448. doi: 10.1093/bioinformatics/btad448. Bioinformatics. 2023. PMID: 37481709 Free PMC article. - Harnessing CRISPR-Cas systems for bacterial genome editing.
Selle K, Barrangou R. Selle K, et al. Trends Microbiol. 2015 Apr;23(4):225-32. doi: 10.1016/j.tim.2015.01.008. Epub 2015 Feb 17. Trends Microbiol. 2015. PMID: 25698413 Review. - CRISPR/Cas9 for genome editing: progress, implications and challenges.
Zhang F, Wen Y, Guo X. Zhang F, et al. Hum Mol Genet. 2014 Sep 15;23(R1):R40-6. doi: 10.1093/hmg/ddu125. Epub 2014 Mar 20. Hum Mol Genet. 2014. PMID: 24651067 Review.
Cited by
- CRISPR-GRANT: a cross-platform graphical analysis tool for high-throughput CRISPR-based genome editing evaluation.
Fu H, Shan C, Kang F, Yu L, Li Z, Yin Y. Fu H, et al. BMC Bioinformatics. 2023 May 30;24(1):219. doi: 10.1186/s12859-023-05333-w. BMC Bioinformatics. 2023. PMID: 37254060 Free PMC article. - PSReliP: an integrated pipeline for analysis and visualization of population structure and relatedness based on genome-wide genetic variant data.
Solovieva E, Sakai H. Solovieva E, et al. BMC Bioinformatics. 2023 Apr 5;24(1):135. doi: 10.1186/s12859-023-05169-4. BMC Bioinformatics. 2023. PMID: 37020193 Free PMC article. - CRISPR genome editing using computational approaches: A survey.
Alipanahi R, Safari L, Khanteymoori A. Alipanahi R, et al. Front Bioinform. 2023 Jan 11;2:1001131. doi: 10.3389/fbinf.2022.1001131. eCollection 2022. Front Bioinform. 2023. PMID: 36710911 Free PMC article. Review. - Evaluation of genome and base editing tools in maize protoplasts.
Fierlej Y, Jacquier NMA, Guille L, Just J, Montes E, Richard C, Loue-Manifel J, Depège-Fargeix N, Gaillard A, Widiez T, Rogowsky PM. Fierlej Y, et al. Front Plant Sci. 2022 Nov 28;13:1010030. doi: 10.3389/fpls.2022.1010030. eCollection 2022. Front Plant Sci. 2022. PMID: 36518521 Free PMC article. - Computational Tools and Resources for CRISPR/Cas Genome Editing.
Li C, Chu W, Gill RA, Sang S, Shi Y, Hu X, Yang Y, Zaman QU, Zhang B. Li C, et al. Genomics Proteomics Bioinformatics. 2023 Feb;21(1):108-126. doi: 10.1016/j.gpb.2022.02.006. Epub 2022 Mar 24. Genomics Proteomics Bioinformatics. 2023. PMID: 35341983 Free PMC article. Review.
MeSH terms
LinkOut - more resources
Full Text Sources
Other Literature Sources