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. 2014 Oct 15;30(20):2968-70.
doi: 10.1093/bioinformatics/btu427. Epub 2014 Jul 1.

Genome Editing Assessment Using CRISPR Genome Analyzer (CRISPR-GA)

Free PMC article

Genome Editing Assessment Using CRISPR Genome Analyzer (CRISPR-GA)

Marc Güell et al. Bioinformatics. .
Free PMC article


Summary: Clustered regularly interspaced short palindromic repeats (CRISPR)-based technologies have revolutionized human genome engineering and opened countless possibilities to basic science, synthetic biology and gene therapy. Albeit the enormous potential of these tools, their performance is far from perfect. It is essential to perform a posterior careful analysis of the gene editing experiment. However, there are no computational tools for genome editing assessment yet, and current experimental tools lack sensitivity and flexibility. We present a platform to assess the quality of a genome editing experiment only with three mouse clicks. The method evaluates next-generation data to quantify and characterize insertions, deletions and homologous recombination. CRISPR Genome Analyzer provides a report for the locus selected, which includes a quantification of the edited site and the analysis of the different alterations detected. The platform maps the reads, estimates and locates insertions and deletions, computes the allele replacement efficiency and provides a report integrating all the information.

Availability and implementation: CRISPR-GA Web is available at Documentation on CRISPR-GA instructions can be found at



Fig. 1.
Fig. 1.
CRISPR-GA pipeline. (A) From experiment to report. Schematic pipeline of gene editing assessment. (B) Output of CRISPR-GA: different information is estimated. Deletions, insertions, HR and corresponding efficiencies. Upper panels estimate the number of insertions and deletions and each corresponding size. Middle panels estimate the number of insertions and deletions, and their corresponding location within the genomic locus of interest. The bottom panel shows the number of deletions and HR at each corresponding locations and outputs the HR and NHEJ efficiency. (C) Experimental results assessed by CRISPR-GA from testing several mutants of cas9, gRNAs and a DNA template. HR and NHEJ values are presented

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