CRISPR-DAV: CRISPR NGS data analysis and visualization pipeline.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 28961906.
- Also identified by DOI 10.1093/bioinformatics/btx518.
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Abstract
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. 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/. xuning.wang@bms.com.
Medical subject headings
- Clone Cells
- Clustered Regularly Interspaced Short Palindromic Repeats
- High-Throughput Nucleotide Sequencing
- INDEL Mutation
- Sequence Analysis, DNA
- Software