Both On and Off target

• open in new windowBenchling
• open in new windowCrispor
• open in new windowCrista
• open in new windowRGEN Tools
• open in new windowCRISPR-GE

On Target (Positive) Selection

• open in new windowCRISPick (formerly sgRNA Designer, same algorithm)
• open in new windowSSC - Sequence Scan for CRISPR

Off Target

Web Servers:

• open in new windowE-CRISP
• open in new windowCHOPCHOP
• open in new windowCCTop
• open in new windowCRISPRdirect
• open in new windowPhyto CRISP-Ex
• open in new windowZiFiT
• open in new windowGT-Scan
• open in new windowCOSMID
• open in new windowflyCRISPR targetFinder
• open in new windowCRISPR-PLANT v2
• open in new windowYeast CRISPRi

Commercial sites (though free):

• open in new windowIDT
• open in new windowSynthego
• open in new windowDNA 2.0
• open in new windowDharmacon

Prime Editing

• http://easy-prime.cc/
• https://pegit.giehmlab.dk/
• http://pegfinder.sidichenlab.org/
• https://primeedit.nygenome.org/
• https://fgcz-shiny.uzh.ch/PnBDesigner/
• https://primedesign.pinellolab.partners.org/
• https://aceofbases.cos.uni-heidelberg.de/index.html
• https://gt-scan.csiro.au/petal/submit

Cas13

• http://deepcas13.weililab.org/
• http://rna-targeting-design.org/custom
• https://github.com/Janga-Lab/CASowary

Downloadable programs:

• open in new windowsgRNAcas9
• open in new windowCasOT

Check mutations: NGS

• open in new windowCRISPR-GA

Check mutations: Sanger Sequencing

• open in new windowTIDE
• open in new windowDSDecodeM
• open in new windowICE Analysis

Silent mutations

• open in new windowWatCut

Codon Optimization

• open in new windowCodon Optimization Tool (IDT)

Information Resources

• open in new windowGenome Engineering (Zhang Lab)
• open in new windowaddgene CRISPR Resource
• open in new windowflyCRISPR
• open in new windowiGTRCN CRISPR/Cas Web Resources
• open in new windowPlantGenome Editing Database
• open in new windowCRISPR-Cas.org (Joung Lab)