Genome editing assessment software tools | Genome engineering data analysis
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.
Allows quantification and visualization of CRISPR-Cas9 outcomes, as well as evaluation of effects on coding sequences, noncoding elements and selected off-target sites. CRISPResso is a suite of computational tools that offers several 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, and distinction between non-homologous end joining (NHEJ), homology-directed repair (HDR), and mixed mutation events.
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.
An online tool that is able to separate chromatogram data containing ambiguous base calls into wild-type and mutant allele sequences, revealing the nature of the indel from a single sequencing run per individual performed directly on a PCR product spanning the targeted site, without cloning. Poly Peak Parser facilitates rapid identification and sequence characterization of heterozygous mutant carriers generated by genome editing.
Contains several tools for analyzing Sanger Sequencing data files in R, including reading .scf and .ab1 files, making basecalls and plotting chromatograms. sangerseqR offers functions to generate a chromatogram from a sangerseq class object, to run the Poly Peak Parser shiny app in the systems default browser, to allow the user to retrieve results from and assign values to sangerseq-class objects and many others.
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.
Furnishes a method for identifying and reporting indel mutations and other precise genome editing events. BATCH-GE can compute the corresponding mutagenesis efficiencies for a large number of samples in parallel. Furthermore, it enables assessment of homology-directed repair (HDR)-mediated precise genome editing experiments by returning efficiencies for one or multiple intended base pair substitutions.