Comprehensive Bioinformatics Tools for CRISPR/Cas9 Design and Analysis

October 10, 2024 Off By admin

CRISPR/Cas9 technology has revolutionized genome editing, enabling precise modifications of genetic material in a wide range of organisms. To facilitate the design, execution, and analysis of CRISPR experiments, various bioinformatics tools and software have been developed. These tools assist researchers in multiple stages of the CRISPR workflow, from designing optimal guide RNAs (gRNAs) to analyzing results from high-throughput sequencing.

Tools for CRISPR/ Cas9

Software / Tool	Category	Free	Tool Description	Link
Off-Spotter	Genomics	yes	Off spotter helps in the design of optimal “guide” RNAs (gRNAs) by providing several protospacer adjacent motif (PAM) choices, a run-time definition of the seed and of the allowed number of mismatches.	Link
CrispRVariants	Genomics	yes	CrispRVariants resolves and localizes individual mutant alleles with respect to the endonuclease cut site. Individual variant alleles from either traditional Sanger sequencing or high-throughput CRISPR-Cas9 mutagenesis sequencing experiments can be quantified and visualized. CrispRVariants allows 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.	Link
CRISPOR	Genomics	yes	CRISPOR assists with guide selection in 120 genomes, including plants and many emerging model organisms, and pre-calculated results for all human coding exons as a UCSC Genome Browser track. Enhanced off-target prediction accuracy.	Link
Breaking CAS	Genomics	yes	Breaking CAS is a versatile system for detecting putative sgRNA off-targets in CRISPR/Cas applications. BreakingCas allows working with all eukaryotic genomes available in the ENSEMBL database, for a detailed inspection of the genomic neighbourhood of every single potential off-target so as to qualitatively assess them. This web server allows specifying the characteristics and parameters of the nuclease to be used, although predefined set are available for several popular Cas proteins.	Link
CRISPR-AnalyzeR for pooled screens caRpools	High-throughput Sequencing	yes	CaRpools is an R package for exploratory data analysis providing CRISPR/Cas9 screen analysis. CaRpools integrates screening documentation and generation of standardized analysis reports. Its open virtual appliance allows analysis without prior programming knowledge and is therefore suited for novice and expert users.	Link
Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout MAGeCK	High-throughput Sequencing	yes	MAGeCK identifies positively and negatively selected sgRNAs and genes in genome-scale CRISPR/Cas9 knockout experiments. The workflow can be partitioned into four steps: read count normalization, mean-variance modeling, sgRNA ranking and gene ranking. MAGeCK outperforms existing computational methods in its control of the false discovery rate (FDR) and its high sensitivity.	Link
ScreenBEAM	High-throughput Sequencing	yes	Screening Bayesian Evaluation and Analysis Method (ScreenBEAM) is an R package to do gene-level meta-anlaysis of high-throughput functional genomics RNAi or CRISPR screening data.	Link
HiTSelect	High-throughput Sequencing	yes	A comprehensive analysis pipeline for rigorously selecting screen hits and identifying functionally relevant genes and pathways by addressing off-target effects, controlling for variance in both gene silencing efficiency and sequencing depth of coverage and integrating relevant metadata. HiTSelect is implemented as an open-source package, with a user-friendly interface for data visualization and pathway exploration.	Link
CRISPRs	High-throughput Sequencing	yes	CRISPRs enables the detection of CRISPRs in locally-produced data and consultation of CRISPRs present in the database. If CRISPR-associated (cas) genes are annotated the program will show them as well.	Link