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CRISPR/Cas9 sgRNA design software tools | Genome engineering

The Type II clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system is an adaptive immune response in prokaryotes, protecting host cells against invading phages or plasmids by cleaving these foreign DNA species in a targeted…
CasBLASTR
Web

CasBLASTR

Identifies and designs sgRNA sites for the engineered variants and orthogonal…

Identifies and designs sgRNA sites for the engineered variants and orthogonal Cas9 nucleases. CasBLASTR allows to annotate CRISPR-Cas9 target sites for a given input sequence. This tool accepts…

ProtospacerWB
Desktop

ProtospacerWB Protospacer Workbench

An offline software application for rapid, flexible design of Cas9 sgRNA in one…

An offline software application for rapid, flexible design of Cas9 sgRNA in one or more target sites, for any CRISPR application in any organism where a full or at least partial reference assembly is…

CRISPR design
Web

CRISPR design

A web tool crafted to simplify the process of CRISPR guide selection in an…

A web tool crafted to simplify the process of CRISPR guide selection in an input DNA sequence by (i) discovering possible offtargets genome-wide, (ii) highlighting guides with high target…

E-CRISP
Web

E-CRISP

A software tool to design and evaluate target sites for use with the Clustered…

A software tool to design and evaluate target sites for use with the Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) system.

sgRNA Scorer
Web
Desktop

sgRNA Scorer

Allows users to identify single guide RNA (sgRNA) sites for any protospacer…

Allows users to identify single guide RNA (sgRNA) sites for any protospacer adjacent motif (PAM) sequence of interest. sgRNA Scorer predictions has been validated in human cells across multiple…

CRISPRscan
Web

CRISPRscan

A predictive single guide RNAs (sgRNA)-scoring algorithm that effectively…

A predictive single guide RNAs (sgRNA)-scoring algorithm that effectively captures the sequence features affecting the activity of CRISPR-Cas9 in vivo. Based on a large scale analysis of sgRNA…

CLD
Desktop

CLD CRISPR library designer

Aims to the design of custom single guide RNA (sgRNA) libraries for all…

Aims to the design of custom single guide RNA (sgRNA) libraries for all organisms with annotated genomes. CLD is suitable for the design of libraries using modified CRISPR enzymes and targeting…

OutKnocker
Web

OutKnocker

Facilitates the analysis of deep sequencing data to identify knockout cells…

Facilitates the analysis of deep sequencing data to identify knockout cells obtained from designer nuclease-mediated genome editing. OutKnocker is a web-based application that allows the detection of…

Breaking-Cas
Web

Breaking-Cas

Detects putative sgRNA off-targets in CRISPR/Cas applications. BreakingCas…

Detects putative sgRNA off-targets in CRISPR/Cas applications. BreakingCas allows working with all eukaryotic genomes available in the ENSEMBL database, while other existing tools can only work with…

Cas-Designer
Desktop
Web

Cas-Designer

A user-friendly program to aid researchers in choosing appropriate target sites…

A user-friendly program to aid researchers in choosing appropriate target sites in a gene of interest for type II CRISPR/Cas-derived RNA-guided endonucleases (RGENs), which are now widely used for…

CRISPR-DO
Web
Desktop

CRISPR-DO

A web application for the design and optimization of guide sequences that…

A web application for the design and optimization of guide sequences that target both coding and non-coding regions in spCas9 CRISPR system across human, mouse, zebrafish, fly and worm genomes.…

predictSGRNA
Desktop

predictSGRNA

Enables to predict single guide RNA (sgRNA) target sequences efficiency.…

Enables to predict single guide RNA (sgRNA) target sequences efficiency. PredictSGRNA implements an algorithm based on position-dependent dinucleotide model. This tool is an R package implementing…

CRISPOR
Web
Desktop

CRISPOR

A web-based tool to assist with guide selection in 120 genomes, including…

A web-based tool to assist 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…

CASPER
Desktop

CASPER CRISPR Associated Software for Pathway Engineering and Research

Allows analysis of on and off-target activity in any organism with any Cas…

Allows analysis of on and off-target activity in any organism with any Cas enzyme. CASPER is a method that implements flexible algorithms to guide precise genome editing. The software can perform…

GuideScan
Web
Desktop

GuideScan

Allows for the design of CRISPR guide RNA libraries that can be used to edit…

Allows for the design of CRISPR guide RNA libraries that can be used to edit coding and noncoding genomic regions. GuideScan produces high-density sets of guide RNAs (gRNAs) for single- and…

CRISPR-RT
Web

CRISPR-RT CRISPR RNA-Targeting

Helps biologists to design the crRNA with improved target specificity for the…

Helps biologists to design the crRNA with improved target specificity for the CRISPR-C2c2 system. CRISPR-RT is a web service that allows a user to upload an RNA sequence, set specifications according…

SSC
Web

SSC Spacer Scoring for CRISPR

A web application for predicting sgRNA efficiency from spacer sequences. SSC…

A web application for predicting sgRNA efficiency from spacer sequences. SSC supports the applications of optimizing sgRNA libraries in CRISPR/Cas9 knockout or CRISPR/dCas9 inhibition/activation…

WU-CRISPR
Web

WU-CRISPR

A bioinformatics tool for genome-wide design of sgRNAs with improved…

A bioinformatics tool for genome-wide design of sgRNAs with improved efficiency. A custom design interface was established for gRNA selection based on user-provided sequences. The availability of…

CROP-IT
Web

CROP-IT CRISPR/Cas9 Off-target Prediction and Identification Tool

Assists biologists in designing CRISPR/CAS9 sgRNAs, by predicting the…

Assists biologists in designing CRISPR/CAS9 sgRNAs, by predicting the off-target sites and ranking them according to the chances of occurrence. Unlike existing prediction programs that solely use DNA…

CHOPCHOP
Web

CHOPCHOP

A web tool for CRISPR- and TALEN-based genome editing. The overarching…

A web tool for CRISPR- and TALEN-based genome editing. The overarching principle of CHOPCHOP is to provide an intuitive and powerful tool that can serve first time as well as experienced users. The…

CRISPR-FOCUS
Web

CRISPR-FOCUS

Manages SgRNAs’ analysis for Clustered Regularly Interspaced Short…

Manages SgRNAs’ analysis for Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) screen experiments. CRISPR-FOCUS classifies SgRNA and generates evaluations about their efficiency,…

CRISPRpred
Desktop

CRISPRpred

Permits users to predict on-target activity of in-silico sgRNAs efficiently…

Permits users to predict on-target activity of in-silico sgRNAs efficiently based on the applications of Support Vector Machine (SVM) model. This tool provides two key factors that improve the…

CCTop
Desktop
Web

CCTop CRISPR/Cas9 target online predictor

A tool to determine suitable CRISPR/Cas9 target sites in a given query…

A tool to determine suitable CRISPR/Cas9 target sites in a given query sequence(s) and predict its potential off-target sites. CCTop identifies and ranks all candidate sgRNA target sites according to…

Guide Picker
Web

Guide Picker

Allows side-by-side correlative analysis of scoring functions. The CRISPR Guide…

Allows side-by-side correlative analysis of scoring functions. The CRISPR Guide Picker mode is an addition to the DESKGEN Cloud Platform. It allows user to visualize data from four sgRNA design…

CRISPETa
Web

CRISPETa CRISPR Paired Excision Tool

A bioinformatic pipeline for flexible and scalable paired sgRNA design based on…

A bioinformatic pipeline for flexible and scalable paired sgRNA design based on an empirical scoring model. CRISPETa has two useful features: first, it can be used for any number of targets in a…

Cas-Database
Web

Cas-Database

An easy-to-use web-based tool for designing sgRNAs for SpCas9 nucleases on a…

An easy-to-use web-based tool for designing sgRNAs for SpCas9 nucleases on a genome scale. Cas-Database can be applied to construct optimal sgRNA libraries that target thousands of coding sequences…

PITCh designer
Web

PITCh designer Precise Integration into Target Chromosome designer

Designs and performs PITCh knock-in. PITCh designer is a streamlined pipeline…

Designs and performs PITCh knock-in. PITCh designer is a streamlined pipeline developed to automatically design the appropriate microhomologies and the primers to construct locus-specific donor…

AGEseq
Web

AGEseq

AGEseq compares amplicon sequences with expected target sequences and finds…

AGEseq compares amplicon sequences with expected target sequences and finds insertion/deletion sites in the amplicon sequences. AGEseq supports both Sanger and deep-sequencing reads. It is written in…

CRISPRseek
Desktop

CRISPRseek

A highly flexible, open source software package to identify gRNAs that target a…

A highly flexible, open source software package to identify gRNAs that target a given input sequence while minimizing off-target cleavage at other sites within any selected genome. CRISPRseek will…

sgTiler
Desktop

sgTiler

Allows users to create tiling single guide RNAs (sgRNAs) for Clustered…

Allows users to create tiling single guide RNAs (sgRNAs) for Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 system. sgTiler is developed for generating sgRNAs for any input…

CRISPR-DS
Desktop

CRISPR-DS

Allows users to prepare data before performing experiments. CRISPR-DS is a…

Allows users to prepare data before performing experiments. CRISPR-DS is a processing pipeline that permits enrichment by size selection prior to library preparation. The software intends to enhance…

Redkmer
Desktop

Redkmer

Allows users to characterize profused and specific to X-chromosomes short 25bp…

Allows users to characterize profused and specific to X-chromosomes short 25bp sequences (kmers) with XY male karyotypes. Redkmer is a standalone software that provides a pipeline composed of ten…

CRISTA
Web

CRISTA CRISPR Target Assessment

Allows prediction of the cleavage propensity of a genomic site by a given…

Allows prediction of the cleavage propensity of a genomic site by a given single guide RNA (sgRNA). The CRISTA method incorporates a wide range of features specific to the genomic content, features…

FlashFry
Desktop

FlashFry

Allows user to discover and characterize Clustered Regularly Interspaced Short…

Allows user to discover and characterize Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) guide sequences. FlashFry generates a block-compressed binary database of all potential…

CrossCheck
Dataset

CrossCheck

Provides a centralized repository for published datasets. CrossCheck allows…

Provides a centralized repository for published datasets. CrossCheck allows users to compare a user-defined list of gene symbols with the software reference database. The database contains over…

pgRNAFinder
Web

pgRNAFinder

Provides eight vertebrate genomes for guide RNA (gRNA) design. pgRNAFinder…

Provides eight vertebrate genomes for guide RNA (gRNA) design. pgRNAFinder contains three different modules: (1) a single gRNA design module, (2) a short distance paired-gRNA design module and (3) a…

ge-CRISPR
Web

ge-CRISPR

Could be very beneficial to select single sgRNA with high potency from a pool…

Could be very beneficial to select single sgRNA with high potency from a pool of identified sgRNAs. ge-CRISPR is a web server which is an integrated pipeline to predict sgRNAs with high on target and…

EuPaGDT
Web

EuPaGDT Eukaryotic Pathogen gRNA Design Tool

Implements an effective on-target search algorithm to identify gRNA targeting…

Implements an effective on-target search algorithm to identify gRNA targeting multi-gene families, which play important roles in host–pathogen interactions. EuPaGDT assists users in designing…

CRISPR-ERA
Web

CRISPR-ERA CRISPR-mediated Editing, Repression, and Activation

A web tool for automated genome wide single guide RNA (sgRNA) design.…

A web tool for automated genome wide single guide RNA (sgRNA) design. CRISPR-ERA can provide different sgRNA searching approaches for genome editing, such as Cas9 nuclease. In addition, CRISPR-ERA…

CRISPRdirect
Web

CRISPRdirect

A simple and functional web server for selecting rational CRISPR/Cas targets…

A simple and functional web server for selecting rational CRISPR/Cas targets from an input sequence. The CRISPR/Cas system is a promising technique for genome engineering which allows target-specific…

PhytoCRISP-Ex
Web
Desktop

PhytoCRISP-Ex

Provides a reliable and first ever application for predicting CRISPR/Cas9…

Provides a reliable and first ever application for predicting CRISPR/Cas9 targets within various plankton genomes. PhytoCRISP-Ex is also equipped with an easy to use, yet powerful, standalone version…

CRISPR-P
Web

CRISPR-P

A web tool for synthetic single-guide RNA design of CRISPR-system in plants.…

A web tool for synthetic single-guide RNA design of CRISPR-system in plants. CRISPR-P allows users to search for high specificity Cas9 target sites within DNA sequences of interest, which also…

ZiFiT
Web

ZiFiT Zinc Finger Targeter

A simple and intuitive web-based tool that provides an interface to identify…

A simple and intuitive web-based tool that provides an interface to identify potential binding sites for engineered zinc finger proteins (ZFPs), clustered regularly interspaced short palindromic…

CRISPR…
Web

CRISPR multitargeter

A web-based tool for automatic searches of CRISPR guide RNA targets. It can…

A web-based tool for automatic searches of CRISPR guide RNA targets. It can find highly similar or identical target sites in multiple genes or transcripts or design targets unique to particular genes…

Off-Spotter
Web

Off-Spotter

Helps in the design of optimal "guide" RNAs (gRNAs) by providing…

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,…

CRISPy-web
Web

CRISPy-web

Designs single-guide (sgRNA) for any gene/region of interest in user-submitted…

Designs single-guide (sgRNA) for any gene/region of interest in user-submitted genome data. CRISPy-web is implemented as a standalone web application for Cas9 target prediction. It consists of…

CT-Finder
Web

CT-Finder

A web service to help users design guide RNAs (gRNAs) optimized for…

A web service to help users design guide RNAs (gRNAs) optimized for specificity. CT-Finder accommodates the original single-gRNA Cas9 system and two specificity-enhancing paired-gRNA systems: Cas9…

COSMID
Web

COSMID CRISPR Off-target Sites with Mismatches, Insertions, and Deletions

Predicts and ranks potential off-target cleavage sites and provides valuable…

Predicts and ranks potential off-target cleavage sites and provides valuable guidance for guide strand designs. COSMID scores the potential off-target sites based on the number and location of base…

Cas-OFFinder
Desktop
Web

Cas-OFFinder

Searches for potential off-target sites in a given genome or user-defined…

Searches for potential off-target sites in a given genome or user-defined sequences.

GT-Scan
Web

GT-Scan Genome Target Scan

A flexible web-based tool that ranks all potential targets in a user-selected…

A flexible web-based tool that ranks all potential targets in a user-selected region of a genome in terms of how many off-targets they have.

CasOT
Desktop

CasOT

Identifies potential off-target sites of given Cas9/gRNA targets or target…

Identifies potential off-target sites of given Cas9/gRNA targets or target pairs in any user-specified sequence or genome. CasOT is an open-source tool with several tunable parameters like PAM type…

flyCRISPR
Web

flyCRISPR

A web tools for expanded application of the CRISPR/Cas9 system in Drosophila…

A web tools for expanded application of the CRISPR/Cas9 system in Drosophila through homology-directed repair (HDR) with double-stranded DNA (dsDNA) donor templates that facilitate complex genome…

CRISPy
Dataset

CRISPy

Allows rapid identification of sgRNA target sequences in the Chinese hamster…

Allows rapid identification of sgRNA target sequences in the Chinese hamster ovary (CHO-K1) genome. The CRISPy tool identified 1,970,449 CRISPR targets divided into 27,553 genes and lists the number…

sgRNAcas9
Desktop

sgRNAcas9

A software package developed for fast design of CRISPR sgRNA with minimized…

A software package developed for fast design of CRISPR sgRNA with minimized off-target effect, in order to improve CRISPR-Cas9 specificity for targeted genome editing and transcriptional control.

CGAT
Web

CGAT CRISPR Genome Analysis Tool

Identifies potential target sites for CRISPR gene editing in DNA sequences.…

Identifies potential target sites for CRISPR gene editing in DNA sequences. Then, CGAT uses the identified target sequences to search a genome of interest for potential off-target matches. CGAT…

Azimuth
Desktop

Azimuth

Machine learning-based predictive modelling of CRISPR/Cas9 guide efficiency.…

Machine learning-based predictive modelling of CRISPR/Cas9 guide efficiency. Azimuth will allow the broader biological community to accurately identify the best guide for their genes of interest.

DESKGEN
Desktop

DESKGEN

Designs any genome editing experiment in any cell line. DESKGEN is organised…

Designs any genome editing experiment in any cell line. DESKGEN is organised into two modules: “Experiments” and “Repositories” which together provides genome-editing tools. The software can…

SSFinder
Desktop

SSFinder

A comprehensive tool for the identification of specific CRISPR-Cas target sites…

A comprehensive tool for the identification of specific CRISPR-Cas target sites with high reliability. SSFinder is a freeware, easy to edit, and low memory demand tool compatible with many commonly…

CasFinder
Desktop

CasFinder

Finds Cas9 targets in sequence provided by a user that have identified as…

Finds Cas9 targets in sequence provided by a user that have identified as having no off-targets in a specified genome through an algorithm that searches the genome for similar sequences. The…

CRISPR…
Dataset

CRISPR Knockout Guide Designer

Allows users to search from over 100,000 genomes and 9,000 species in order to…

Allows users to search from over 100,000 genomes and 9,000 species in order to make a Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) guide for gene knockout. CRISPR Knockout Guide…

CRISPR gRNA…
Web

CRISPR gRNA Design tool

It lets you design gRNA(s) to engineer your target and minimize off-target…

It lets you design gRNA(s) to engineer your target and minimize off-target effects using DNA2.0 Scoring Algorithms.

Benchling
Web

Benchling

Allows scientists to design, share, and record experiments or tests. The…

Allows scientists to design, share, and record experiments or tests. The Benchling platform contains a Biological Registration System, an Electronic Lab Notebook, and Molecular Biology Design and…

CRISPRer
Web

CRISPRer

A tool for designing CRISPR/Cas protospacers and seeds.

A tool for designing CRISPR/Cas protospacers and seeds.

Cas9 Design
Web

Cas9 Design

A guide RNA sequence design platform for the Cas9/CRISPR silencing system for…

A guide RNA sequence design platform for the Cas9/CRISPR silencing system for model organisms. The platform is easy to use for gRNA design with input query sequences. It finds potential targets by…

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