Table 2:

Subset of available zebrafish CRISPR/Cas tools

Design tools	CRISPRscan	guide RNA design tool and off target prediction	https://www.crisprscan.org/ [87]
	CRISPRon/CRISPRoff	on-target and off-target predictions for CRISPR-Cas9 gene editing	https://rth.dk/resources/crispr/ [92, 93]
	Breaking-Cas	variable design of gRNAs for CRISPR/Cas for all eukaryotic genomes available on Ensembl	https://bioinfogp.cnb.csic.es/tools/breakingcas/ [94]
	CCTop/CRISPRater	tunable CRISPR/Cas target online predictor and effectivity predictor	https://cctop.cos.uni-heidelberg.de/index.html [95, 96]
	AceofBASEs	sgRNA design and off-target prediction tool for adenine and cytosine base editors	https://aceofbases.cos.uni-heidelberg.de/index.html [97]
	CHOPCHOP	CRISPR and TALEN design tool	https://chopchop.cbu.uib.no/ [88, 98, 99]
	CRISPOR	guide RNA design tool and off target prediction	http://crispor.org [100]
	CRISPRdirect	guide RNA design tool and off target prediction	http://crispr.dbcls.jp/ [101]
	CRISPRseek	software package for gRNA design	[102]
	GT-Scan appsuite	gRNA and HDR template design tools(GT-Scan, TUSCAN, CUNE)	https://gt-scan.csiro.au/ [103–105]
	CRISPR RGEN Tools	Tools for RNA-guided endonucleases, including off target prediction, Cas gRNA design, base editing and primer editing tools	http://www.rgenome.net/cas-designer/ [106–110]
	Gene Sculpt Suite	tools for genome editing including design of short oligonucleotides for homology-based gene editing (GtagHD), prediction of extend of microhomology-mediated end joining repair (MEDJED) and prediction of locations with just 1–2 MMEJ alleles (MENTHU)	http://www.genesculpt.org/ [111]
	Mojo Hand	CRISPR and TALEN design tool	https://talendesign.org/ [112, 113]
	CRISPR-ERA	gRNA design tool for genome editing, repression and activation	http://crispr-era.stanford.edu/ [114]
	CRISPR-SKIP	design of exon skipping mutations using single-base editors	https://knoweng-0.igb.illinois.edu/crispr-skip/ [115]
Databases	CRISPRz	database of validated CRISPR targets in zebrafish	https://research.nhgri.nih.gov/CRISPRz/
	iSTOP	database of sgRNAs for generating STOP codons	http://www.ciccialab-database.com/istop [116]
SpCas9 alternatives	Spg	NGN Pam	[117]
	SpRY	NRN PAM	[117]
	LbCpf1 (Cas12a)	TTTV PAM	[118]
	SpCas9 VQR	NGAN, NGNG PAM	[119]
	SpCas9 EQR	NGAG PAM	[119]
	SpCas9 VRER	NGCG PAM	[119]
	SpCas9 KKH	NNNRRT PAM	[120]
	SauCas9	NNGRRT PAM	[121]
	AsCpf1	TTTV PAM	[121]
	Nme2Cas9	NNNNCC PAM	[121]
	ErCas12a	YTTN PAM	[122]
	ScCas9	NNG PAM	[123]
Transgenic lines	4xUAS:NLS-Cas9,myl7:RFP	Gal4 effector line for Cas9 expression with red heart transgenesis marker	[124]
	4xUAS:NLS-Cas9,cryaa:EGFP	Gal4 effector line for Cas9 expression with green eye transgenesis marker	[124]
	hsp70l:LOXP-DsRed-LOXP-Cas9-GFP,rnu6–32:CRISPR1-tyr	Cre and heat shock controlled Cas9-GFP fusion expression	[125]
	ef1a:Cas9-NLS	ubiquitous expression of Cas9	[126]
	actb2:NLS-zCas9-NLS,cryaa:TagRFP	ubiquitous expression of Cas9 with red eye transgenesis marker	[127]
	hsp70l:LOXP-mCherry-LOXP-NLS-zCas9-NLS	Cre and heat shock controlled Cas9 expression	[127]
	ubb:NLS-zCas9-NLS,myl7:EGFP	ubiquitous expression of Cas9 with green heart transgenesis marker	[127]
	hsp70l:Cas9-IRES-EGFP,myl7:EGFP	heat shock inducible co-expression of Cas9 and EGFP with green heart transgenesis marker	[128]
	hsp70l:Cas9-P2A-mCherry,myl7:EGFP	heat shock inducible co-expression of Cas9 and mCherry with green heart transgenesis marker	[128]
	lyzC:Cas9,cryaa:GFP	Neutrophil-specific expression of Cas9 with green eye transgenesis marker	[129]
	hsp70l:zCas9-T2A-GFP,5x(U6:sgRNA)	heat shock inducible simultaneous expression of Cas9 and GFP, ubiquitous expression 5 guide RNAs for lineage tracing using GESTALT	[130]
	hsp70l:DsRed-v7,myl7:EGFP	CRISPR array, with green heart transgenesis marker for lineage tracing using GESTALT	[130]
	UAS:Cas9T2AGFP;U6:sgRNA1;U6:sgRNA2	Gal4 effector line for simultaneous Cas9 and GFP expression	[131]
Base editors (BE)	BE4max	cytosine BE	[132]
	zABE7.10	adenine BE	[133]
	BE, BE-VQR, dBE-VQR	cytosine BE	[134]
	zAncBE4max	cytosine BE	[135]
	BE4-Gam	cytosine BE	[97, 136]
	ABE8e	adenine BE	[97]
	ancBE4max-SpymacCas9	cytosine BE	[136]
	ancBE4max	cytosine BE	[97, 132, 136]
	evoBE4max	cytosine BE	[97]
	CBE4max-SpRY	cytosine BE	[137]
	zAncBE4max	cytosine BE	[135]
Transcriptional regulators	dCas9-KRAB	repressor	[138]
	dCas9-VP160	activator	[138]
	dCas9-Eve	repressor	[139]
Lineage tracing	GESTALT (genome editing of synthetic target arrays for lineage tracing)	lineage tracing through modification of a CRISPR/Cas target array	[140]
	scGESTALT (single-cell GESTALT)	GESTALT combined with transcriptome profiling	[130]
	LINNAEUS (lineage tracing by nuclease-activated editing of ubiquitous sequences)	lineage tracing through Cas9 induced INDELs in a multicopy transgene combined with transcriptome profiling	[141]
	ScarTrace	lineage tracing through Cas9 induced INDELs in a multicopy transgene combined with transcriptome profiling	[142]
Screening tools	MIC-Drop (multiplexed intermixed CRISPR droplets)	microfluidics based generation of a library of droplets containing different RNP complexes together with DNA barcodes for injection	[86]