Table 2.

List of CRISPR/Cas outcome analysis tools

Type	Name	Description	Website	Web server or standalone tool	Ref.
Decoding Sanger sequencing of on-target sites	TIDE	Quantifying non-templated CRISPR/Cas9 mutations	https://tide.nki.nl	Web server	[103]
	TIDER	Quantifying the indels of templated CRISPR/Cas9 editing	https://tide.nki.nl	Web server	[105]
	EditR	Quantifying base editing results	https://baseeditr.com/	Standalone tool	[159]
	Poly peak parser	Quantifying heterozygous indels	http://yost.genetics.utah.edu/software.php	Standalone tool	[160]
	DSDecode	Automatically decoding the sequencing chromatograms	http://skl.scau.edu.cn/dsdecode/	Standalone tool	[107]
NGS evaluation of targeted amplicon sequences	BATCH-GE	Detecting the on- and off-target impacts by analyzing deep sequencing data and calculating mutagenesis efficiencies	https://github.com/WouterSteyaert/BATCH-GE	Standalone tool	[115]
	CRISPR-GA	Quantifying and characterizing indels and homologous recombination events	https://crispr-ga.net	Web server	[108]
	CRISPResso2	Enabling the users to analyze, visualize, and compare CRISPR outputs from hundreds of experiments using batch functionality	https://crispresso.pinellolab.partners.org/submission	Web server	[110]
	Cas-Analyzer	Measuring the frequencies of mutations induced by CRISPR/Cas9 and other programmable nucleases for NGS data analysis	http://www.rgenome.net/cas-analyzer/	Web server	[109]
	CRIS.py	Providing a Python-based software to analyze NGS data for both knockout and knock-in (multiple users specified) modifications from one to thousands of samples at once	https://github.com/patrickc01/CRIS.py; https://s.stjude.org/video/player.html?videoId=6000021936001	Standalone tool	[111]
	CRISPRpic	Providing precise mutation calling and ultrafast analysis of the sequencing results	https://github.com/compbio/CRISPRpic	Web server	[161]
	CRISPR-DAV	Providing high-throughput analysis of amplicon-based NGS data	https://github.com/pinetree1/crispr-dav	Standalone tool	[162]
	GNL-Scorer	Combining optimal datasets, models, and features, to address the cross-species problem	https://github.com/TerminatorJ/GNL_Scorer	Standalone tool	[114]
	CrispRVariants	Quantifying Sanger sequencing and high-throughput amplicon sequencing	https://www.bioconductor.org/packages/CrispRVariants	Standalone tool	[112]
NGS evaluation of pooled CRISPR/Cas9 libraries	CRISPRCloud2	Providing accurately mapping short reads to CRISPR library; statistically aggregating the information across multiple sgRNAs targeting the same gene; providing a user-friendly data visualization and query interface; easy linking with other tools and bioinformatic resources for target preference	https://crispr.nrihub.org	Web server	[125]
	CRISPRAnalyzeR	Featuring with eight hit calling strategies including DESeq2, MAGeCK, edgeR, sgRSEA, Z-Ratio, Mann-Whitney test, ScreenBEAM, and BAGEL; exploring the pooled CRISR/Cas9 screens	https://www.crispr-analyzer.org; https://www.github.com/boutroslab/CRISPRAnalyzeR	Standalone tool	[123]
	PinAPL-Py	Providing a comprehensive workflow covering quality control, automated sgRNA sequence extraction and alignment, sgRNA enrichment/depletion analysis, and gene ranking	https://pinapl-py.ucsd.edu	Web server	[124]
	MAGeCK	Providing analysis of large-scale screens	https://bitbucket.org/liulab/mageck/src/master/	Standalone tool	[117]
	MAGeCK-VISPR	Providing analysis of large-scale screens	https://bitbucket.org/liulab/mageck-vispr	Standalone tool	[163]
	BAGEL	Providing analysis of large-scale screens	https://bagel-for-knockout-screens.sourceforge.net/	Standalone tool	[121]
	HiTSelect	Providing analysis of large-scale screens	https://github.com/diazlab/HiTSelect	Standalone tool	[119]
	caRpools	Providing analysis of large-scale screens	https://github.com/boutroslab/caRpools	Standalone tool	[118]
	CHANGE-seq	Measuring the genome-wide activity of Cas9		Standalone tool	[130]
	ScreenBEAM	Providing analysis of large-scale screens	https://github.com/jyyu/ScreenBEAM	Standalone tool	[120]
	CERES	Providing CRISPR screen analysis	https://depmap.org/ceres/	Standalone tool	[164]
	PBNPA	Providing analysis of large-scale screens	https://cran.r-project.org/web/packages/PBNPA/	Standalone tool, database	[122]
NGS evaluation of off-target effects	DISCOVER-Seq	Detecting unbiasedly off-targets by precise tracking of MRE11; exploring molecular nature of Cas activity in cell with single-base resolution	N/A	Standalone tool	[129]
	HTGTS	Providing robust detection of DSBs generated by engineered nucleases based on their translocation to other endogenous or ectopic DSBs	weblogo.berkeley.edu	Standalone tool	[165]
	IDLVs	Detecting off-target cleavages with a frequency as low as 1%; providing frequent off-target sites up to 13 mismatches between the sgRNA and its genomic target	N/A	Standalone tool	[127]
	BLESS	Mapping DNA DSBs at nucleotide resolution by detecting telomere ends, Sce endonuclease-induced DSBs, and complex genome-wide DSB landscapes	N/A	Standalone tool
	BLISS	Measuring the location and frequency of DSBs in genome by direct labeling of DSBs in fixed cells or tissues; quantifying DSBs through unique molecular identifiers; low input requirement	N/A	Standalone tool	[166]
	GUIDE-seq	Providing unbiased and global detection of DSBs induced by CRISPR RNA-guided nucleases	N/A	Standalone tool	[69]
	GOTI	Providing comparison of edited and non-edited cells distinguished by Cre-loxP recombination system	https://github.com/sydaileen/GOTI-seq	Standalone tool	[167]
	SITE-Seq	Identifying off-targets in vitro by integrating biochemical assay to increase the enrichment of CRISPR/Cas cleavage fragments	N/A	Standalone tool	[168]
	Digenome-seq	Providing deep sequencing of in vitro Cas9-digested genomes	N/A	Standalone tool	[169]
	CRISPR-net	Quantifying CRISPR off-target activities with mismatches and indels	https://codeocean.com/capsule/9553651/tree/v1	Standalone tool	[170]
	CIRCLE-seq	Providing a sensitive and unbiased in vitro genome-wide off-target identification strategy optimized by using restriction enzyme for circularization of randomly sheared genome DNA	N/A	Standalone tool	[128]
Evaluation and prediction of repair outcomes	inDelphi	Predicting the mutational outcomes	https://www.crisprindelphi.design/	Web server, database	[86]
	SPROUT	Predicting the length, probability, and sequences of indels caused by CRISPR/Cas gene editing	https://zou-group.github.io/SPROUT	Web server	[113]

Note: DSB, double strand break; NGS, next-generation sequencing.