Table 1 A Survey of CRISPR design tools
ToolTypeWeb InputWeb batch entry?Consider variant?Variant specific designs compared to SNP-CRISPRURL/Reference
CHOPCHOPweb-basedGene, Genome coordinatesNoNoNonechopchop.rc.fas.harvard.edu (Labun et al. 2019)
GuideScanweb-basedGene, Genome coordinatesYesNoNoneguidescan.com (Perez et al. 2017)
DRSC find CRISPR Toolweb-basedGene, Genome coordinatesNoNoNoneflyrnai.org/crispr (Housden et al. 2015)
E-CRISPRweb-basedGene, SequenceNoPossibleFewerae-crisp.org (Heigwer et al. 2014)
CRISPORweb-basedGene, SequenceNo (seq) Yes (gene)PossibleSameacrispor.tefor.net (Haeussler et al. 2016)
CRISPRscanweb-basedbGene, SequenceNoPossibleFeweracrisprscan.org (Moreno-Mateos et al. 2015)
CRISPRdirectweb-basedGene, SequenceNoPossibleSameacrispr.dbcls.jp (Naito et al. 2015)
CRISPR-ERAweb-basedGene, Sequence, Genome coordinatesNoNoNonecrispr-era.stanford.edu (Liu et al. 2015)
CRISPR-DTweb-basedSequenceNoNoNonebioinfolab.miamioh.edu/CRISPR-DT (Zhu and Liang 2019)
DeepCRISPRweb-basedSequenceNoUndeterminedcdeepcrispr.net (Chuai et al. 2018)
GT-Scanweb-basedSequenceNoPossibleSameagt-scan.csiro.au/ (Oliveros et al. 2016)
GPP sgRNA Designerweb-basedGene, SequenceYesPossibleSameaportals.broadinstitute.org/gpp/public/analysis-tools/sgrna-design (Sanson et al. 2018)
CCTopweb-basedSequenceYesPossibleSameacrispr.cos.uni-heidelberg.de (Stemmer et al. 2015)
Cas-Designerweb-basedSequenceYesPossibleSameargenome.net/cas-designer (Park et al. 2015)
CRISPR Optimal Target Finderweb-basedSequenceNoPossibleSameatargetfinder.flycrispr.neuro.brown.edu (Gratz et al. 2014)
Breaking-Casweb-basedbSequenceYesPossibleSameabioinfogp.cnb.csic.es/tools/breakingcas (Oliveros et al. 2016)
Off-Spotterweb-basedbSequenceNoPossibleSameacm.jefferson.edu/Off-Spotter (Pliatsika and Rigoutsos 2015)
ProtospacerGUI (OSX only)NANANoNoneprotospacer.com
CrisPamcommand lineNANAUndeterminedcgithub.com/ristllin/CrisPam (Rabinowitz et al. 2019)
CRISPRseekcommand lineNANAPossibleSameabioconductor.org/packages/release/bioc/html/CRISPRseek.html (Zhu et al. 2014)
AlleleAnalyzercommand lineNANAYesSamegithub.com/keoughkath/AlleleAnalyzer (Keough et al. 2019)
SNP-CRISPRweb-basedbVariants (e.g., VCF file)YesYesNAflyrnai.org/tools/snp_crispr
  • Note: We limited our survey to CRISPR design tools that do not require registration or user login.

  • a Users need to provide flanking sequence and filter out irrelevant designs.

  • b A command line version is also available.

  • c Test was attempted but results were not obtained.