Table 1 Open in new tab Representative...

Table 1

Representative tools for high-throughput genome-editing systems

Tool	Remarks	Websites	References
gRNA-designer	Guide RNA design tool	https://portals.broadinstitute.org/gpp/public/analysis-tools/gRNA-design	Doench et al. (2016)
CHOPCHOP version 2		http://chopchop.cbu.uib.no	Labun et al. (2016)
E-CRISP		http://www.e-crisp.org/E-CRISP/index.html	Heigwer et al. (2014)
CRISPR Library Designer		https://github.com/boutroslab/cld	Heigwer et al. (2016)
Guide Picker		https://www.deskgen.com/guide-picker/	Hough et al. (2017)
GUIDES		https://github.com/sanjanalab/GUIDES	Meier et al. (2017)
CRISPR-P version 2.0		http://cbi.hzau.edu.cn/crispr/	Liu et al. (2017a, 2017b)
flyCRISPR		http://tools.flycrispr.molbio.wisc.edu/targetFinder/	Gratz et al. (2014)
EuPaGDT		http://grna.ctegd.uga.edu/index.html	Peng and Tarleton (2015)
CRISPR-local		http://crispr.hzau.edu.cn/CRISPR-Local/	Sun et al. (2019)
WU-CRISPR		http://crisp r.wustl.edu	Wong et al. (2015)
gRNA Scorer version 2.0		https://crisp r.med.harva rd.edu/gRNA ScorerV2/	Chari et al. (2017)
CRISPRpred		https://github.com/khaled-buet/CRISPRpred	Rahman and Rahman (2017)
DeepCRISPR		http://www.deepcrispr.net/	Chuai et al. (2018)
DeepSpCas9		http://deepcrispr.info/DeepSpCas9	Kim et al. (2019a, 2019b)
DeepHF		http://www.DeepHF.com/	Wang et al. (2019a, 2019b)
CRISPRon		https://rth.dk/resources/crispr/	Xiang et al. (2021)
GuideScan		http://www.guidescan.com/	Perez et al. (2017)
CRISPOR version 2		http://crispor.tefor.net/crispor.cgi	Haeussler et al. (2016)
CRISPRscan		http://www.crisprscan.org/	Moreno-Mateos et al. (2015)
CRISPRitz	Predicts potential off-target sites in the genome	https://github.com/pinellolab/CRISPRitz	Cancellieri et al. (2020)
CRISPR-PLANT version 2		http://www.genome.arizona.edu/crispr2/	Minkenberg et al. (2019)
CCTop		https://crisp r.cos.uni-heidelberg.de/index.html	Stemmer et al. (2015)
CROP-IT		http://cheetah.bioch.virginia.edu/AdliLab/CROP-IT/homepage.html	Singh et al. (2015)
CASPER		https://github.com/TrinhLab/CASPER	Mendoza and Trinh (2018)
CT-Finder		http://bioinfolab.miamioh.edu/ct-finder	ZHu et al. (2016)
CRISPR-GA	Track on-target mutation patterns	http://crispr-ga.net	Güell et al. (2014)
caRpools		http://github.com/boutroslab/caRpools	Winter et al. (2016)
CRISPResso		http://github.com/lucapinello/CRISPResso	Pinello et al. (2016)
Cas-Analyser		http://www.rgenome.net/cas-analyzer	Park et al. (2017a, 2017b)
CrispRVariants		https://www.bioconductor.org/packages/CrispRVariants	Lindsay et al. (2016)
MAGeCK-VISPR		http://bitbucket.org/liulab/mageck-vispr	Li et al. (2015)
PinAPL-Py		http://pinapl-py.ucsd.edu	Spahn et al. (2017)
CRISPRAnalyzeR		http://www.github.com/boutroslab/CRISPRAnalyzeR	Winter et al. (2017)
AGEseq		http://aspendb.uga.edu/ageseq	Xue and Tsai (2015)
UDiTaS		https://github.com/editasmedicine/uditas	Giannoukos et al. (2018)
Hi-TOM		http://www.hi-tom.net/hi-tom/	Liu et al. (2019)
CRIS.py		https://github.com/patrickc01/CRIS.py	Connelly and Pruett-Miller (2019)
GUIDE-seq	Detect off-target mutations	—	Tsai et al. (2015)
LAM-HTGTS		http://robinmeyers.github.io/transloc_pipeline/	Hu et al. (2016)
Digenome-seq		—	Kim et al. (2015)
DISCOVER-Seq		—	Wienert et al. (2019)
OffScan		—	Cui et al. (2020)
FED	Detect foreign element	http://www.hi-tom.net/FED	Liu et al. (2021)
INSIDER	Detect foreign element	https://github.com/aehrc/INSIDER	Tay et al. (2021)

Tool	Remarks	Websites	References
gRNA-designer	Guide RNA design tool	https://portals.broadinstitute.org/gpp/public/analysis-tools/gRNA-design	Doench et al. (2016)
CHOPCHOP version 2		http://chopchop.cbu.uib.no	Labun et al. (2016)
E-CRISP		http://www.e-crisp.org/E-CRISP/index.html	Heigwer et al. (2014)
CRISPR Library Designer		https://github.com/boutroslab/cld	Heigwer et al. (2016)
Guide Picker		https://www.deskgen.com/guide-picker/	Hough et al. (2017)
GUIDES		https://github.com/sanjanalab/GUIDES	Meier et al. (2017)
CRISPR-P version 2.0		http://cbi.hzau.edu.cn/crispr/	Liu et al. (2017a, 2017b)
flyCRISPR		http://tools.flycrispr.molbio.wisc.edu/targetFinder/	Gratz et al. (2014)
EuPaGDT		http://grna.ctegd.uga.edu/index.html	Peng and Tarleton (2015)
CRISPR-local		http://crispr.hzau.edu.cn/CRISPR-Local/	Sun et al. (2019)
WU-CRISPR		http://crisp r.wustl.edu	Wong et al. (2015)
gRNA Scorer version 2.0		https://crisp r.med.harva rd.edu/gRNA ScorerV2/	Chari et al. (2017)
CRISPRpred		https://github.com/khaled-buet/CRISPRpred	Rahman and Rahman (2017)
DeepCRISPR		http://www.deepcrispr.net/	Chuai et al. (2018)
DeepSpCas9		http://deepcrispr.info/DeepSpCas9	Kim et al. (2019a, 2019b)
DeepHF		http://www.DeepHF.com/	Wang et al. (2019a, 2019b)
CRISPRon		https://rth.dk/resources/crispr/	Xiang et al. (2021)
GuideScan		http://www.guidescan.com/	Perez et al. (2017)
CRISPOR version 2		http://crispor.tefor.net/crispor.cgi	Haeussler et al. (2016)
CRISPRscan		http://www.crisprscan.org/	Moreno-Mateos et al. (2015)
CRISPRitz	Predicts potential off-target sites in the genome	https://github.com/pinellolab/CRISPRitz	Cancellieri et al. (2020)
CRISPR-PLANT version 2		http://www.genome.arizona.edu/crispr2/	Minkenberg et al. (2019)
CCTop		https://crisp r.cos.uni-heidelberg.de/index.html	Stemmer et al. (2015)
CROP-IT		http://cheetah.bioch.virginia.edu/AdliLab/CROP-IT/homepage.html	Singh et al. (2015)
CASPER		https://github.com/TrinhLab/CASPER	Mendoza and Trinh (2018)
CT-Finder		http://bioinfolab.miamioh.edu/ct-finder	ZHu et al. (2016)
CRISPR-GA	Track on-target mutation patterns	http://crispr-ga.net	Güell et al. (2014)
caRpools		http://github.com/boutroslab/caRpools	Winter et al. (2016)
CRISPResso		http://github.com/lucapinello/CRISPResso	Pinello et al. (2016)
Cas-Analyser		http://www.rgenome.net/cas-analyzer	Park et al. (2017a, 2017b)
CrispRVariants		https://www.bioconductor.org/packages/CrispRVariants	Lindsay et al. (2016)
MAGeCK-VISPR		http://bitbucket.org/liulab/mageck-vispr	Li et al. (2015)
PinAPL-Py		http://pinapl-py.ucsd.edu	Spahn et al. (2017)
CRISPRAnalyzeR		http://www.github.com/boutroslab/CRISPRAnalyzeR	Winter et al. (2017)
AGEseq		http://aspendb.uga.edu/ageseq	Xue and Tsai (2015)
UDiTaS		https://github.com/editasmedicine/uditas	Giannoukos et al. (2018)
Hi-TOM		http://www.hi-tom.net/hi-tom/	Liu et al. (2019)
CRIS.py		https://github.com/patrickc01/CRIS.py	Connelly and Pruett-Miller (2019)
GUIDE-seq	Detect off-target mutations	—	Tsai et al. (2015)
LAM-HTGTS		http://robinmeyers.github.io/transloc_pipeline/	Hu et al. (2016)
Digenome-seq		—	Kim et al. (2015)
DISCOVER-Seq		—	Wienert et al. (2019)
OffScan		—	Cui et al. (2020)
FED	Detect foreign element	http://www.hi-tom.net/FED	Liu et al. (2021)
INSIDER	Detect foreign element	https://github.com/aehrc/INSIDER	Tay et al. (2021)

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