Genome Editing Software Guide

Welcome to Genome Editing Software Guide

We are collecting information on software for Genome Editing.
Our collection is over 200 tools (551 tools at 2025/2/21 UPDATE). So you can find good tools supporting your research.

If there is a comment, I would be happy if you contact us:
Administrator: Kazuki Nakamae, Ph.D. : e-mail: kazukinakamae_at_mark_gmail.com
bonohu lab, Genome Editing Innovation Center, Hiroshima University, Japan

Citation info:
We described this webpage in the following review:
Nakamae, K. and Bono, H. Genome editing and bioinformatics. Gene and Genome Editing, 100018 (2022).

Table of contents

Target Design

Target Design for CRISPR-Cas system

Web tools

  1. blastn
  1. Cas-OFFinder - RGEN Tools
  1. COSMID
  1. CRISPR Optimal Target Finder(flyCRISPR)
  1. CRISPR-P
  1. CRISPR-Plant
  1. E-CRISP (The German Cancer Research Center, 🇩🇪)
  1. GT-Scan ([Institute for Molecular Bioscience]（https://imb.uq.edu.au）, 🇦🇺)
  1. Cas-Designer - RGEN Tools
  1. CRISPR MultiTargeter
  1. CRISPR-ERA (Bioinformatics Department, 🇨🇳)
  1. CRISPRdirect
  1. CRISPRscan (Giraldez Lab, Yale University, 🇺🇸)
  1. DRSC Find CRISPRs (DRSC/TRiP Functional Genomics Resources, Harvard Medical School, 🇺🇸)
  1. EuPaGDT (Tarleton Research Group, The Center for Tropical and Emerging Global Diseases, The University of Georgia, 🇺🇸)
  1. Off-Spotter
  1. Spacer Scoring for CRISPR(SSC) (Cistrome Project, 🇺🇸)
  1. Wellcome Sanger Institute Genome Editing(WGE) (Wellcome Sanger Institute, 🇬🇧)
  1. WU-CRISPR (Xiaowei lab, 🇺🇸)
  1. Breaking-Cas (BioinfoGP!, 🇪🇸)
  1. CRISPy-web (DTU Biosustain, Technical University of Denmark, 🇩🇰)
  1. Machine learning-based end-to-end CRISPR/Cas9 guide design （Microsoft Research, 🇺🇸)
  1. phytoCRISP-Ex (Institut de Biologie de l’ENS (IBENS), 🇫🇷)
  1. CINDEL (Bioinformatics & Genomics (BIG) Lab, 🇰🇷)
  1. CRISPR-FOCUS (Xiaole Shirley Liu lab, Harvard University & Dana-Farber Cancer , 🇺🇸)
  1. CRISPETa(CRG Bioinformatics Core Facility, 🇪🇸)
  1. CRISTA (Mayrose lab, 🇮🇱)
  1. Green listed (Wermeling lab, Karolinska Institutet, 🇸🇪)
  1. GUIDES (Sanjana lab, 🇺🇸)
  1. PITCh designer 2.0 (Yamamoto lab, Hiroshima University, Japan🇯🇵)
  1. sgRNA Scorer 2.0 (FNLCR, 🇺🇸)
  1. CCTop (Centre for Organismal Studies, 🇩🇪)
  1. CRISPOR (TEFOR, 🇫🇷)
  1. CRISPR-DT (Liang Lab, 🇺🇸)
  1. DeepCpf1(Laboratory of Genome Editing & Data Science & Artificial Intelligence Laboratory, 🇰🇷)
  1. DeepCRISPR (Bioinformatics department, Tongji University, 🇨🇳)
  1. MENTHU - Gene Sculpt Suite (Gene Sculpt Suite, Iowa State University & Mayo Clinic, 🇺🇸)
  1. TUSCAN (CSIRO, 🇦🇺)
  1. CHOPCHOP (Valen lab, 🇳🇴)
  1. CrisPam (Dani Offen Group, Telaviv University, 🇮🇱)
  1. CRISPR-Local(National Key Laboratory of Crop Genetic Improvement & Center for Bioinformatics, Huazhong Agricultural University, 🇨🇳)
  1. CUNE (CSIRO, AEHRC, 🇦🇺)
  1. DeepHF (State Key Laboratory of Genetic Engineering, Fudan University, 🇨🇳)
  1. KOnezumi (生命科学動物資源センター, Tsukuba University, 🇯🇵)
  1. PAVOOC (ETH Zurich, 🇨🇭)
  1. Slice It (Janga lab, Indiana University system, 🇺🇸)
  1. WheatCRISPR (National Research Council Canada, 🇨🇦)
  1. AsCRISPR (National Clinical Research Center for Geriatric Disorders, Central South University, 🇨🇳)
  1. CRISpy-pop
  1. DeepSpCas9variants (Laboratory of Genome Editing, Yonsei University, 🇰🇷)
  1. MMEJ-KO
  1. SNP-CRISPR (DRSC/TRiP Functional Genomics Resources, Harvard Medical School, 🇺🇸)
  1. CRISPick (GPP sgRNA Designer) (Broad Institute, 🇺🇸)
  1. CRISPR-Cereal (National Key Laboratory of Crop Genetic Improvement, Center for Bioinformatics, Huazhong Agricultural University, 🇨🇳)
  1. CRISPR GuideXpress
  1. CRISPR Knock-in Designer
  1. CRISPR-PN2 (O’Halloran lab, The George Washington University, 🇺🇸)
  1. GTagHD - Gene Sculpt Suite (Gene Sculpt Suite, Iowa State University & Mayo Clinic, 🇺🇸)
  1. GuideMaker (United States Department of Agriculture - Agricultural Research Service (USDA-ARS), United States Department of Agriculture, 🇺🇸)
  1. Plant-Crispr (Institute of Botany, Chinese Academy of Sciences, 🇨🇳)
  1. CRISPRedict
  1. CRISPRon
  1. GuideScan2 (Leslie lab & Ventura lab, 🇺🇸)
  1. GuideScan2
  1. CRISPR-AIdit(AIdit-Crispr)
  1. TransCRISPR
  1. AlPaCas
  1. AutoESDCas
  1. Fragmid
  1. CRISPR-COPIES
  1. CRISPR-TE
  1. protoSpaceJAM
  1. StreptoCAD
  1. Alt-R™ (IDT) (IDT, 🇺🇸)
  • The publication is not found.
  1. ATUM (ATUM, 🇺🇸)
  • The publication is not found.
  1. CRISPR Design Tool (Horizon Discovery Ltd, 🇬🇧)
  • The publication is not found.
  1. CRISPR Targeted Gene Designer (Horizon Discovery Ltd, 🇬🇧)
  • The publication is not found.
  1. GT-Scan2 ([Institute for Molecular Bioscience]（https://imb.uq.edu.au）, 🇦🇺)
  • The publication is not found.
  1. Knockout Guide Design - Synthego (Synthego, 🇺🇸)
  • The publication is not found.

CLI tools

C/C++

  1. Crisflash
  1. uCRISPR
  1. SeqCor
  1. CracklingPlusPlus

R

  1. CRISPRseek
  1. CRISPR Library Designer (CLD)
  1. CRISPRpred
  1. predictSGRNA
  1. crispRdesignR
  1. crisprVerse
  1. bluntPred
  1. crisprCHOPOFF

python

  1. SSFinder
  1. SSFinder
  1. Azimuth
  1. Elevation‐search(dsNickFury3)
  1. getCRISPRY
  1. GuideScan
  1. pgRNADesign
  1. pgRNAFinder
  1. CNN_std
  1. CRISPR-SURF
  1. crisproff
  1. DeepCRISPR
  1. Elevation
  1. Elevation‐search(dsNickFury3)
  1. off_target_prediction
  1. predictCRISPR
  1. sgRNA-cleavage-activity-prediction
  1. TUSCAN
  1. AlleleAnalyzer
  1. DeepSgrnaBacteria
  1. AttnToCrispr_CNN
  1. AlleleAnalyzer
  1. SynergizingCRISPR
  1. CrisPam
  1. CRISPR-ONT & CRISPR-OFFT
  1. CNN_predict
  1. AttCRISPR
  1. AddTag
  1. dl-offtarget
  1. CROP
  1. Hi-CRISPR
  1. sgRNACNN
  1. VaLiAnT
  1. BoostMEC
  1. CNN-XG
  1. CRISPR-Cas9-energy-study
  1. Rule Set 3
  1. seq2seq-attention
  1. CRISPRedict
  1. CROPSR
  1. DeepGuide
  1. DeepGuide Reborn
  1. GuideVar
  1. MOFF
  1. piCRISPR
  1. CRISPR-IP
  1. SpCas9_kinetic_model_dashboard
  1. HyenaDNA
  1. CRISOT
  1. CRISPR-HW
  1. Uni-deepSG
  1. CRISOT
  1. CRISPR-DIPOFF
  1. CRISPR-MCA
  1. ARTEMIS
  1. DeepCRISTL
  1. crispAI
  1. CRISPR-Bulge
  1. CRISPert
  1. CRISPR-BERT
  1. CRISPR-M
  1. GuideVar
  1. AddTag
  1. CRISPR-DIPOFF
  1. DeepGuide Reborn
  1. CRISPR-IP
  1. DeepCRISTL
  1. CRISPR-HW
  1. Uni-deepSG
  1. CRISPR-DIPOFF
  1. CRISPR-MCA

perl

  1. sgRNAcas9 - BiooTools
  1. GRIBCG
  1. sgDesigner

Julia

  1. CHOPOFF

JavaScript

  1. Guide Picker (DeskGen, 🇬🇧)

JAVA

  1. SWOffinder

Scala

CALITAS

Application

  1. Protospacer Workbench
  1. CASPER
  1. OffRisk

Pipeline

  1. Crackling
  1. CRISPRitz
  1. CRISPR-SE
  1. BoostMEC
  1. Elektrum
  1. MuRCiS_pipeline
  1. Auto-MuRCiS Pipeline
  1. beroukhim-lab/ancestry_manuscript_code
  1. CRISPR_PAM
  1. PathoGD

Target Design for TALEN

Web tools

  1. TAL Effector Nucleotide Targeter 2.0
  1. E-TALEN

CLI tools

JAVA

  1. TALENoffer

Target Design for ZFN

Web tools

  1. ZFN-Site

Target Design for Base Editing

Web tools

  1. iSTOP
  1. BE-Designer
  1. BE-FF
  1. CRISPR-CBEI
  1. DeepBaseEditor
  1. DeepHF - BEdeepon
  1. ACEofBASEs
  1. CRISPR-BETS
  1. DeepHF - BEdeepoff
  1. BES-Designer

CLI tools

  1. Base editing prediction model
  1. beditor
  1. beditor
  1. autocbei
  1. AMINEsearch
  1. DeepBE
  1. EPCNNBE
  1. KOnezumi-AID

Target Design for Prime Editing

Web tools

  1. pegFinder (Sidi Chen lab, Yale University, 🇺🇸)
  1. Prime Editing Design Tool(Primeedit) (Sanjana lab, The New York Genome Center & New York University, 🇺🇸)
  1. DeepPE (Hyongbum Henry Kim Lab, Yonsei University, 🇰🇷)
  1. Easy-Prime (Cheng Lab, St. Jude Children’s Research Hospital, 🇺🇸)
  1. PE-Designer - RGEN Tools (Molecular Genome Engineering, Hanyang University, 🇰🇷)
  1. pegIT (Department of Biomedicine, Aarhus University, 🇩🇰)
  1. pegLIT (Liu lab, Broad Institute, 🇺🇸)
  1. PEselector
  1. PETaL
  1. PlantPegDesigner (State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences, 🇨🇳)
  1. PnB Designer
  1. Prime-del (Shendure lab, University of Washington, 🇺🇸)
  1. PrimeDesign
  1. DeepPrime
  1. MinsePIE
  1. OPED
  1. ePRIDICT
  1. PRIDICT2.0
  1. SynDesign

CLI tools

Python

  1. MinsePIE
  1. PINE-CONE
  1. GenET
  1. PRIDICT
  1. DTMP-prime

Target Design for Cas13

Web tools

  1. CRISPR-RT
  1. Cas13design
  1. CasRx guide design
  1. Deep Learning-Powered Cas13d Guide Design
  1. TIGER

CLI tools

Python

  1. CASowary

Target Design for TnpB

Web tools

1.TEEP

Prediction for indel disribution

Web tools

  1. Microhomology-Predictor
  1. FORECasT
  1. inDelphi
  1. MEDJED - Gene Sculpt Suite
  1. SPROUT
  1. BE-Hive
  1. VBC-Score
  1. BE-DICT
  1. CGBE-SMART
  1. FORECasT-BE
  1. BE_Endo

CLI tools

R

  1. MEDJED

Python

  1. inDelphi-model
  1. SelfTarget
  1. Lindel
  1. CROTON
  1. MENdel
  1. Apindel

Prediction for gene expression after genome editing

CLI tools

Applications

  1. EXPosition

Prediction for RNA off-target induced by Base Editors

CLI tools

Python

  1. RNAOffScan v1 (STL model)
  1. RNAOffScan v2 (SNL model)

TIDE Analysis

Web tools

  1. Poly Peak Parser
  1. TIDE
  1. CRISP-ID
  1. TIDER
  1. EditR
  1. Indigo - GEAR-GENOMICS
  1. DECODR
  1. ICE Analysis
  1. PtWAVE

CLI tools

R

  1. EditR

Sequencing Analysis

NGS Analysis for DNA amplicon sequencing

Web tools

  1. CRISPR-GA
  1. Outknocker 2
  1. AGEseq
  1. Cas-Analyzer
  1. BE-Analyzer - RGEN tools
  1. CRISPAltRations(rhAmpSeq™ CRISPR Analysis Tool) login required
  1. CRISPResso2
  1. Hi-TOM
  1. CLiCKAR
  1. CRISPR-Sub - RGEN Tools
  1. GOANA
  1. PE-Analyzer - RGEN Tools (Molecular Genome Engineering, Hanyang University, 🇰🇷)
  1. CRISPR-Analytics (CRISPR-A)
  1. CrisprStitch
  1. GMUSCLE

CLI tools

R

  1. CrispRVariants
  1. AlleleProfileR
  1. amplican

python

  1. CRISPResso
  1. CRISPRMatch
  1. Cortado
  1. CRIS.py
  1. CRISPResso2
  1. knock-knock
  1. MAUND
  1. superQ
  1. crispr-DART
  1. CRISPRpic
  1. CRISPECTOR
  1. GOANA
  1. CRISPECTOR2.0
  1. MKSR_off_targets

Perl

  1. ampliconDIVider
  1. CRISPR-DAV

JAVA

  1. SIQ

Julia

  1. Massively_RGN_OTs

Pipeline

  1. BATCH-GE
  1. R2-analysis/amplicon-seq
  1. CRISPRamplicon - BiooTools
  • The publication is not found.

Application

  1. CRISPR-GRANT

NGS Analysis for unbiased DNA off-target detection

Web tools

  1. Digenome-seq web tool

CLI tools

Perl

  1. transloc_pipeline
  1. BLENDER
  1. GOTI
  1. CAST-Seq

Python

  1. guideseq(GUIDE-Seq)
  1. CIRCLE-seq
  1. EndoV-seq
  1. CHANGE-seq
  1. Digenome toolkit
  1. CRISPECTOR
  1. Digenome-toolkit ver2.
  1. PEGUIDE (PEACSeq)
  1. TAPE-seq_flanking_depth
  1. OFF-TRACKER
  1. OliTag-seq

R

  1. CAST-Seq
  1. breakinspectoR

Pipeline

  1. iGUIDE
  1. Galaxy for Cut Site Detection
  1. BreakTag
  1. CRIT-Seq

NGS Analysis for WGS

Web tools

  1. sINSIDER

CLI tools

C++

  1. GenEditScan

Python

  1. INSIDER
  1. SeqVerify

RNA-seq analysis for Genome Editing

CLI tools

R

  1. Synergy analysis

Python

  1. CRISPR-GEM

Pipeline

  1. CRISPRroots
  1. DANGER analysis
  1. PiCTURE

Hi-C analysis for Genome Editing

CLI tools

Python

  1. 3density

long-read seqeuncing analysis

CLI tools

Python

  1. greporeseq

Perl

  1. InSiDeR

Pipeline

  1. Knock-knock
  1. VAULT
  1. CRISPRnano
  1. DAJIN
  1. DAJIN2
  1. ltschmitt/ZF-rec_analyses

Featurizing design of genome editing

CLI tools

Python

  1. RIsearch
  1. MaChIAto
  1. sglearn

Excel Macro

  1. RIMA v2

CRISPR screen

pooled CRISPR screen

Web tools

  1. CRISPRcloud
  1. PinAPL-Py
  1. VISPR-online
  1. CRISPRcleanRWebApp
  1. FSsgRNA-Analyzer

CLI tools

R

  1. CaRpools
  1. ScreenBEAM
  1. PBNPA
  1. bcSeq
  1. CRISPRcleanR
  1. CRISPhieRmix
  1. CB2
  1. drugZ
  1. GEMINI
  1. MAGeCKFlute
  1. gscreend
  1. CoRe
  1. Orthrus
  1. CRISPR-StAR
  1. MultiPerturb-seq (MPS)
  1. CERES
  • The publication is not found.
  1. gCrisprTools
  • The publication is not found.

python

  1. BAGEL
  1. casTLE
  1. STARS
  1. pyCRISPRcleanR
  1. JACKS
  1. CSC
  1. Chronos
  1. DSCN
  1. poola
  1. crispr-bean (BEAN)

JAVA

  1. PoolQ

matlab

  1. HitSelect

GENE-Eextensions

  1. RIGER

Pipeline

  1. MAGeCK
  1. MAGeCK-VISPR
  1. scMAGeCK
  1. CombiPIPE
  1. CERES inference
  1. CRISPRmap-Pipeline

simulator for pooled CRISPR screen

CLI tools

R

  1. CRSsim
  1. arrayedCRISPRscreener

Julia

  1. CRISPulator

Tiling CRISPR screen

CLI tools

R

  1. RELICS

Pipeline

  1. PASTMUS

Automated Design of Gene-Editing Experiments

CLI tools

LLM Prompt

X.CRISPR-GPT

CRISPR Biology

CRISPR array

Web tools

  1. CRISPRTarget
  1. CRISPRDetect
  1. HMMCAS
  1. CRISPRCasFinder [online]
  1. CRISPRminer
  1. CRISPRCasTyper
  1. CRISPR Spacer Database and Exploration Tool
  1. CRISPRloci

CLI tools

C/C++

  1. PILER-CR
  1. Crass

JAVA

  1. CRT
  1. CRISPRAlign
  1. metaCRT
  1. MinCED

python

  1. CRISPRleader
  1. metaCRISPR
  1. CRISPRdisco
  1. SPADE
  1. CRISPRcasIdentifier
  1. CRISPRIdentify
  1. Casboundary
  1. CrisprOpenDB
  1. CrisprVi
  1. PAMpredict

Perl

  1. CRISPRDirection
  1. CRISPRdigger
  1. MetaCRAST

R

  1. CRISPRclassify
  1. Spacer2PAM

annotation, mapping, lineage analysis of CRISPR array

Web tools

  1. CRISPRcompar - CRISPRdb
  1. CRISPRmap
  1. CRISPRone

CLI tools

Shell Script

  1. SpacerPlacer
  1. PAMPHLET

Shell Script

  1. ConsPred

Anti-CRISPR (Acr)

Web tools

  1. AcrFinder
  1. PaCRISPR

CLI tools

python

  1. AcrFinder
  1. Anti-CRISPR
  1. AcrNET(DeepAcr)
  1. DeepAcr
  1. PreAcrs

Protein design associated with genome editing

CLI tools

python

  1. ProteinMPNN
  1. ProGen2
  1. esm
  1. EVOLVEpro
  1. Evo
  1. evo/semantic_mining
  1. PE-SB

Phenotypic Analysis

Gene Analysis

Web tools

  1. NEST

CLI tools

python

  1. CRaftID

Jupyter Notebook

  1. sc_eVIP

Gene Function Analysis using Genome Editing

CLI tools

R

  1. CCS

Database

Web tools

  1. CRISPRs Database(CRISPRdb)
  1. CRISPI
  1. Cas-Database - RGEN Tools
  1. CRISPRz
  1. grID
  1. UCSC genome browser - CRISPR Targets Track
  1. PICKLES
  1. Anti-CRISPRdb
  1. Cpf1-Database - RGEN Tools
  1. DepMap
  1. CasPDB
  1. CRISPRlnc
  1. MHcut Browser
  1. Project Score (Sanger DepMap)
  1. AcrDB
  1. BioGRID Open Repository of CRISPR Screens (ORCS)
  1. CEN‐tools
  1. CRISPR atlas
  1. CRISP-View
  1. CRISPRCasdb
  1. dbGuide
  1. AcrHub
  1. COMBAT crRNA Repository (Stanley Qi Lab, Stanford University, 🇺🇸)
  1. crisprSQL
  1. iCSDB
  1. Repair-seq data browser
  1. BE-SCAN
  1. BEvariants
  1. CRISPRbase
  1. CRISPRDB
  1. GEM
  1. CasPEDIA Database
  1. CRISPRlipid
  1. ShinLib - interactive gene fitness analysis
  1. Be-dataHIVE
  1. CRISPRals
  1. VDGE
  1. CRISPRoffT
  1. PerturbDB
  1. Validated gRNA Target Sequences
  • The publication is not found.

CLI tools

  1. PyCEN

Files

  1. SiMul-db
  1. PROTECTiO_db_v1_0_0

Benchmarking dataset

CLI tools

python

  1. BEACON
  1. CRISPR_Data_Imbalance
  1. HiroshimaUniv_PtBio Benchmarking Dataset

Integrated Platform

Web tools

  1. CRISPR-GE
  1. Benchling
  • The publication is not found.

Educational software for genome editing

Web tools

  1. CRISPectra

CRISPR-based Lineage tracing

Scala

  1. Cas9FateMapping (GESTALT)

Python

  1. TraceQC
  1. FRACTAL
  1. PRESUME

R

  1. DNA Typewriter
  1. Sciphy

MATLAB

  1. xzhanglab/CRISPR-based-Lineage-Tracing-Simulation

Other tools involved with CRISPR science

Web tools

  1. indCAPS
  1. BAR-Seq
  1. CReVIS-Seq - RGEN Tools
  1. CRISPRcruncher

CLI tools

R

  1. CSESA
  1. MAUDE

Python

  1. Cleavage Site Investigator（CSI）
  1. CReVIS-Seq
  1. CRISPRbuilder-TB
  1. trace
  1. TRACEseq
  1. RunMLDE_SpCas9
  1. GEARS

Pipeline

  1. CASANOVA-C3
  1. capTEtools

Files

  1. DMOS_data

Non-available tools for us (2024/02/05)

  1. CROP-IT
  1. C-SVR Crispr
  1. R-CRISPR
  1. CEDA
  1. ZFDesign
  1. Crispr-SGRU
  1. CrnnCrispr
  1. DeepFM-Crispr
  1. DeepIndel

Inaccessible tools (from Japan)

  1. CRISPRFinder
  1. Zinc Finger Targeter(ZiFiT)
  1. PREP Suite
  1. Mojo Hand
  1. PROGNOS
  1. SAPTA
  1. CrisprGE
  1. DSDecode
  1. CT-Finder (Liang Lab, 🇺🇸)
  1. FlashFry
  1. TAG-IN (Pollard lab, The University of Edinburgh, 🇬🇧)
  1. BEable-GPS
  1. DL-CRISPR
  1. CRISPR-SE
  1. Anti-CRISPRdb v2.2
  1. CRISPR-VAE
  1. ExsgRNA
  1. SynBioStrainFinder
  1. ABSOLVE-seq
  1. EasyDesign
  1. DeepHF - BeStop
  • The publication is not found.
  1. The Genome Targeting Catalogue
  • The publication is not found.