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 (422 tools at 2023/9/9 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. CRISPOR（TEFOR, 🇫🇷）
  1. CHOPCHOP（Valen lab, 🇳🇴）
  1. E-CRISP（The German Cancer Research Center, 🇩🇪）
  1. GUIDES（Sanjana lab, 🇺🇸）
  1. GuideScan2（Leslie lab & Ventura lab, 🇺🇸）
  1. GT-Scan（[Institute for Molecular Bioscience]（https://imb.uq.edu.au）, 🇦🇺）
  1. GT-Scan2（[Institute for Molecular Bioscience]（https://imb.uq.edu.au）, 🇦🇺）
  1. CRISPick (GPP sgRNA Designer)（Broad Institute, 🇺🇸）
  1. IDT（IDT, 🇺🇸）
  1. Knockout Guide Design - Synthego（Synthego, 🇺🇸）
  1. Breaking-Cas（BioinfoGP!, 🇪🇸）
  1. CRISPR Design Tool（Horizon Discovery Ltd, 🇬🇧）

Horizon Discovery - [webserver] - It provides an intuitive one-stop location for guide RNA design and ordering. Use the design tool to order guide RNAs for targeted gene knockout or HDR-mediated genome editing.

  1. CRISPR Targeted Gene Designer（Horizon Discovery Ltd, 🇬🇧）
  1. CT-Finder（Liang Lab, 🇺🇸）
  1. PAVOOC（ETH Zurich, 🇨🇭）
  1. Wellcome Sanger Institute Genome Editing(WGE)（Wellcome Sanger Institute, 🇬🇧）
  1. Cas-Designer - RGEN Tools（Molecular Genome Engineering, 🇰🇷）
  1. CRISPR-ERA（Bioinformatics Department, 🇨🇳）
  1. Spacer Scoring for CRISPR(SSC)（Cistrome Project, 🇺🇸）
  1. WU-CRISPR（Xiaowei lab, 🇺🇸）
  1. TUSCAN（CSIRO, 🇦🇺）
  1. CCTop（Centre for Organismal Studies, 🇩🇪）
  1. CRISTA（Mayrose lab, 🇮🇱）
  1. CINDEL(Bioinformatics & Genomics (BIG) Lab, 🇰🇷)
  1. DeepCpf1（Laboratory of Genome Editing & Data Science & Artificial Intelligence Laboratory, 🇰🇷）
  1. CRISPR-DT（Liang Lab, 🇺🇸）
  1. DeepCRISPR（Bioinformatics department, Tongji University, 🇨🇳）
  1. DeepSpCas9variants（Laboratory of Genome Editing, Yonsei University, 🇰🇷）
  1. DeepHF（State Key Laboratory of Genetic Engineering, Fudan University, 🇨🇳）
  1. sgRNA Scorer 2.0（FNLCR, 🇺🇸）
  1. ATUM（ATUM, 🇺🇸）
  1. CRISPETa(CRG Bioinformatics Core Facility, 🇪🇸)
  1. AsCRISPR（National Clinical Research Center for Geriatric Disorders, Central South University, 🇨🇳）
  1. SNP-CRISPR（DRSC/TRiP Functional Genomics Resources, Harvard Medical School, 🇺🇸）
  1. CrisPam（Dani Offen Group, Telaviv University, 🇮🇱）
  1. CRISPR MultiTargeter
  1. DRSC Find CRISPRs（DRSC/TRiP Functional Genomics Resources, Harvard Medical School, 🇺🇸）
  1. CRISPR Optimal Target Finder(flyCRISPR)（Brown University, 🇺🇸）
  1. CRISPRscan（Giraldez Lab, Yale University, 🇺🇸）
  1. CRISPR-P（National Key Laboratory of Crop Genetic Improvement & Center for Bioinformatics, Huazhong Agricultural University, 🇨🇳）
  1. WheatCRISPR（National Research Council Canada, 🇨🇦）
  1. CRISPR-Local(National Key Laboratory of Crop Genetic Improvement & Center for Bioinformatics, Huazhong Agricultural University, 🇨🇳)
  1. CRISPR-Plant（The Pennsylvania State University and Arizona Genomics Institute, 🇺🇸）
  1. EuPaGDT（Tarleton Research Group, The Center for Tropical and Emerging Global Diseases, The University of Georgia, 🇺🇸）
  1. CRISPy-web（DTU Biosustain, Technical University of Denmark, 🇩🇰）
  1. phytoCRISP-Ex（Institut de Biologie de l’ENS (IBENS), 🇫🇷）
  1. Green listed（Wermeling lab, Karolinska Institutet, 🇸🇪）
  1. CRISPR-FOCUS（Xiaole Shirley Liu lab, Harvard University & Dana-Farber Cancer , 🇺🇸）
  1. Slice It（Janga lab, Indiana University system, 🇺🇸）
  1. PITCh designer 2.0（Yamamoto lab, Hiroshima University, Japan🇯🇵）
  1. GTagHD - Gene Sculpt Suite（Gene Sculpt Suite, Iowa State University & Mayo Clinic, 🇺🇸）
  1. TAG-IN（Pollard lab, The University of Edinburgh, 🇬🇧）
  1. CUNE（CSIRO, AEHRC, 🇦🇺）
  1. MENTHU - Gene Sculpt Suite（Gene Sculpt Suite, Iowa State University & Mayo Clinic, 🇺🇸）
  1. CRISPR-PN2（O’Halloran lab, The George Washington University, 🇺🇸）
  1. CRISPR-Cereal（National Key Laboratory of Crop Genetic Improvement, Center for Bioinformatics, Huazhong Agricultural University, 🇨🇳）
  1. Plant-Crispr（Institute of Botany, Chinese Academy of Sciences, 🇨🇳）
  1. GuideMaker（United States Department of Agriculture - Agricultural Research Service (USDA-ARS), United States Department of Agriculture, 🇺🇸）
  1. KOnezumi（生命科学動物資源センター, Tsukuba University, 🇯🇵）
  1. Machine learning-based end-to-end CRISPR/Cas9 guide design （Microsoft Research, 🇺🇸）
  1. blastn
  1. COSMID
  1. CRISPRdirect
  1. Off-Spotter
  1. Cas-OFFinder - RGEN Tools
  1. ExsgRNA
  1. GuideScan2
  1. CRISPRedict
  1. CRISPR GuideXpress
  1. CRISPR Knock-in Designer
  1. CRISPR-SE
  1. VaLiAnT
  1. Hi-CRISPR
  1. iGOWS
  1. CRISpy-pop

CLI tools

C/C++

  1. Crisflash
  1. uCRISPR
  1. SeqCor

R

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

python

  1. GuideScan
  1. AlleleAnalyzer
  1. pgRNAFinder
  1. TUSCAN
  1. off_target_prediction
  1. GNL_Scorer
  1. SSFinder
  1. getCRISPRY
  1. CRISPR TRAP-seq
  1. pgRNADesign（X. Shirley Liu Lab, Harvard University, 🇺🇸）
  1. CRISPR-SURF
  1. sgRNA-cleavage-activity-prediction
  1. DeepSgrnaBacteria
  1. AttnToCrispr_CNN
  1. CRISPR-ONT & CRISPR-OFFT
  1. Azimuth
  1. Elevation
  1. Elevation-search(dsNickFury3)
  1. CNN_predict
  1. BoostMEC
  1. Rule Set 3
  1. CRISPR-Cas9-energy-study
  1. CROPSR
  1. seq2seq-attention
  1. DeepCRISPR
  1. CNN-XG
  1. AttCRISPR
  1. AlleleAnalyzer
  1. SSFinder
  1. CRISPRedict
  1. GNL-Scorer
  1. crisproff
  1. CNN_std
  1. CRISPR-Net
  1. MOFF
  1. piCRISPR
  1. AddTag
  1. dl-offtarget
  1. CROP
  1. Hi-CRISPR
  1. sgRNACNN
  1. Elevation-search(dsNickFury3)
  1. predictCRISPR
  1. SynergizingCRISPR
  1. CrisPam
  1. CRISPR‐TAPE
  1. C-RNNCrispr
  1. CnnCrispr
  1. CNN-SVR
  1. CGD
  1. ChangeLocator

perl

  1. sgRNAcas9 - BiooTools
  1. GRIBCG
  1. sgDesigner

JavaScript

  1. Guide Picker（DeskGen, 🇬🇧）

Scala

CALITAS

Application

  1. Protospacer Workbench
  1. CASPER

Pipeline

  1. CRISPRitz

  2. Crackling

  1. CRISPR-SE

Target Design for TALEN

Web tools

  1. TAL Effector Nucleotide Targeter 2.0
  1. E-TALEN
  1. Mojo Hand
  1. SAPTA

CLI tools

JAVA

  1. TALENoffer

Target Design for ZFN

Web tools

  1. ZFN-Site

Target Design for Base Editing

Web tools

  1. BE-Designer

  1. BEable-GPS
  1. BE-FF
  1. DeepHF - BEdeepon
  1. DeepHF - BEdeepoff
  1. DeepHF - BeStop
  1. iSTOP
  1. DeepBaseEditor
  1. CRISPR-CBEI
  1. CRISPR-BETS
  1. ACEofBASEs

CLI tools

  1. Base editing prediction model
  1. beditor
  1. beditor
  1. AMINEsearch
  1. autocbei
  1. DeepBE

Target Design for Prime Editing

Web tools

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

CLI tools

  1. MinsePIE
  1. PRIDICT

Target Design for Cas13

Web tools

  1. CRISPR-RT
  1. Cas13design
  1. CasRx guide design
  1. Cas13d guide design
  1. TIGER

CLI tools

  1. CASowary

Prediction for indel disribution

Web tools

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

CLI tools

R

  1. MEDJED

Python

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

Prediction for restriction endonuclease site after genome editing

Web tools

  1. CRISPRcruncher

TIDE Analysis

Web tools

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

CLI tools

R

  1. EditR

Sequencing Analysis

NGS Analysis for DNA amplicon sequencing

Web tools

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

CLI tools

R

  1. CrispRVariants
  1. amplican
  1. AlleleProfileR

python

  1. CRISPResso
  1. CRISPResso2
  1. CRISPRMatch
  1. CRIS.py
  1. CRISPRpic
  1. crispr-DART
  1. knock-knock
  1. superQ
  1. CRISPECTOR
  1. MAUND

Perl

  1. ampliconDIVider
  1. CRISPR-DAV

JAVA

  1. SIQ

Pipeline

  1. BATCH-GE
  1. CRISPRamplicon - BiooTools

Application

  1. CRISPR-GRANT

NGS Analysis for unbiased DNA off-target detection

Web tools

  1. Digenome-seq web tool

CLI tools

Perl

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

Python

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

R

  1. CAST-Seq

Pipeline

  1. iGUIDE

Docker image

  1. Galaxy for Cut Site Detection

RNA-seq analysis for Genome Editing

CLI tools

  1. CRISPRroots
  1. Synergy analysis
  1. DANGER analysis

long-read seqeuncing analysis

CLI tools

Python

  1. greporeseq

Perl

  1. InSiDeR

Pipeline

  1. DAJIN
  1. Knock-knock
  1. VAULT
  1. DAJIN2
  1. CRISPRnano

Featurizing design of genome editing

CLI tools

Python

  1. MaChIAto
  1. sglearn
  1. RIsearch

CRISPR screen

pooled CRISPR screen

Web tools

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

CLI tools

R

  1. gCrisprTools
  1. CaRpools
  1. bcSeq
  1. PBNPA
  1. ScreenBEAM
  1. MAGeCKFlute
  1. CERES
  1. CRISPRcleanR
  1. drugZ
  1. GEMINI
  1. gscreend
  1. Orthrus
  1. CoRe
  1. CB2
  1. CRISPhieRmix

python

  1. BAGEL
  1. pyCRISPRcleanR
  1. JACKS
  1. casTLE
  1. STARS
  1. DSCN
  1. poola
  1. CSC
  1. Chronos

JAVA

  1. PoolQ

matlab

  1. HitSelect

GENE-Eextensions

  1. RIGER

Pipeline

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

simulator for pooled CRISPR screen

CLI tools

R

  1. CRSsim

Julia

  1. CRISPulator

Tiling CRISPR screen

CLI tools

R

  1. RELICS

Pipeline

  1. PASTMUS

RNA editing

Web tools

  1. PREP Suite

CRISPR Biology

CRISPR array

Web tools

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

CLI tools

C/C++

  1. Crass
  1. PILER-CR

JAVA

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

python

  1. SPADE
  1. CRISPRcasIdentifier
  1. CRISPRdisco
  1. metaCRISPR
  1. CRISPRleader
    [Alkhnbashi et al., 2016]
  1. PAMpredict

Ciciani et al., 2022

  1. CrisprVi
  1. CrisprOpenDB
  1. Casboundary
  1. CRISPRIdentify

Perl

  1. MetaCRAST
  1. CRISPRdigger
  1. CRISPRDirection
  1. MetaCRAST

R

  1. Spacer2PAM
  1. CRISPRclassify

Nethery et al., 2021

annotation, mapping, lineage analysis of CRISPR array

Web tools

  1. CRISPRmap
  1. CRISPRone
  1. CRISPRcompar - CRISPRdb

CLI tools

Shell Script

  1. ConsPred

Anti-CRISPR (Acr)

Web tools

  1. AcrFinder
  1. PaCRISPR

CLI tools

python

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

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. UCSC genome browser
  1. grID
  1. Cas-Database - RGEN Tools
  1. dbGuide
  1. CRISPRz
  1. Cpf1-Database - RGEN Tools
  1. MHcut Browser
  1. CRISPRlnc
  1. CRISPRdb
  1. CRISPRCasdb
  1. Anti-CRISPRdb
  1. CRISPI
  1. CasPDB
  1. BioGRID Open Repository of CRISPR Screens (ORCS)
  1. DepMap
  1. CRISPR atlas
  1. Project Score (Sanger DepMap)
  1. PICKLES
  1. CRISP-View
  1. COMBAT crRNA Repository（Stanley Qi Lab, Stanford University, 🇺🇸)
  1. The Genome Targeting Catalogue
  1. CRISPRDB
  1. SynBioStrainFinder
  1. BE-SCAN
  1. BEvariants
  1. Anti-CRISPRdb v2.2
  1. Repair-seq data browser
  1. AcrHub
  1. iCSDB
  1. crisprSQL
  1. AcrDB
  1. CEN‐tools
  1. CRISPRbase
  1. CRISPRbase
  1. ShinLib - interactive gene fitness analysis
  1. CasPEDIA Database
  1. GEM

CLI tools

  1. PyCEN

Integrated Platform

  1. CRISPR-GE
  1. Benchling

Other tools involved with CRISPR science

Web tools

  1. CReVIS-Seq - RGEN Tools

CLI tools

Scala

  1. Cas9FateMapping

R

  1. CSESA
  1. MAUDE

Python

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

Non-available tools for us (2022/11/09)

  1. CEDA
  1. R-CRISPR
  1. C-SVR Crispr
  1. CROP-IT

Inaccessible tools (from Japan)

  1. CRISPRFinder
  1. Zinc Finger Targeter(ZiFiT)：http://zifit.partners.org/ZiFiT/
  1. PROGNOS
  1. CrisprGE
  1. DSDecode
  1. FlashFry
  1. CRISPR-VAE