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Resolves and localizes individual mutant alleles with respect to the endonuclease cut site. CrispRVariants quantifies and visualizes individual variant alleles from either traditional Sanger sequencing or high-throughput CRISPR-Cas9 mutagenesis sequencing experiments. CrispRVariants was designed with interactivity in mind, explicitly allowing users to detect problems and filter sequences appropriately before estimating mutation efficiency. This toolkit can be easily used to create a variant allele summary plot and accompanying table of counts. CrispRVariants enables immediate comparison of variant spectra between target locations.


A tool for batch analysis of next-generation sequencing (NGS) data for genome editing assessment. BATCH-GE detects and reports indel mutations and other precise genome editing events and calculates the corresponding mutagenesis efficiencies for a large number of samples in parallel. This tool will not only contribute to the evaluation of CRISPR/Cas9-based experiments, but will be of use in any genome editing experiment and has the ability to analyze data from every organism with a sequenced genome.

TIDE / Tracking of Indels by DEcomposition

Assesses genome editing of a target locus by CRISPR-Cas9. TIDE quantifies the editing efficacy and simultaneously identifies the predominant types of insertions and deletions (indels) in the targeted pool of cells. The software requires only two standard polymerase chain reactions (PCRs) and two capillary sequencing runs. TIDE can assist in the testing and rational design of genome editing strategies. It is suitable for non-templated Cas9 editing.

CRISPR-GA / CRISPR Genome Analyzer

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.


Allows the quantification of both non-homologous end joining (NHEJ) and homologous directed repair (HDR) occurrences. CRISPResso is a software pipeline for the analysis of targeted CRISPR-Cas9 deep sequencing data. This suite of computational tools provides an integrated, user-friendly interface that can be operated by biologists and bioinformaticians alike. It offers several novel features, including: batch sample analysis via command line interface, integration with other pipelines, tunable parameters of sequence quality and alignment fidelity, discrete measurement of insertions, deletions, and nucleotide substitutions.