Tool name | Description | Input | Output | Maximum mismatches allowed | Supported nucleases | PAM sequence | References |
---|---|---|---|---|---|---|---|
CRISPResso2 | Genome editing and interpretation of amplicon sequencing | 1. Editing of tool specification. 2. Input sequences 3. Amplicon sequence, sgRNA sequence | 1. indel sizes and positions 2. HDR/NHEJ frequency 3. sequence alignment with reference 4. allele-specific quantification | - | Cas9 Cpf1 | NGS | (139) |
Cas-Analyzer | Genome editing and programmable nucleases | 1. Fastq 2. gzip-compressed | 1. indel sizes and positions 2. HDR/NHEJ frequency 3. sequence alignment with reference | up to a 1-nt | SpCas9, StCas9, NmCas9, SaCas9, CjCas9, AsCpf1/LbCpf1, paired nucleases: ZFNs, TALENs, Cas9 nickases, dCas9-FokI | NGS | [140] |
CRISPR-GA | Quantification of the edited site then analysis of the different alterations. | Paired-end reads | 1. indel sizes and positions 2. HDR/NHEJ frequency | < 20 | Cas9 | NGS | [141] |
TIDE/TIDER | Identification of major induced mutations in the editing site using specially developed decomposition algorithm | DNA from a pool of cells treated with RGEN Cas9) and a character string representing the sgRNA sequence (20 nt) | 1. indel sizes and positions 2. HDR/NHEJ frequency | ∼1% | SpCas9, SaCas9, St1Cas9, NmCas9, AsCpf1, FnCpf1, LbCpf1 | Sanger sequencing | [142] [143] |
CRISPR-ERA | Analyze gene editing and gene regulation | Sequence starts with N20NGG | 1. gRNA design 2. E score (efficacy score) 3. S score ( specificity score) 4. E+S score: the sum of efficacy score and Specificity score. | 3 | CRISPR/Cas9 | NGG NAG | [144] |
CRISPRseek | Using various tools for the CRISPR editing including Base Editors and the Prime Editor for input target sequences, | The RNAs sequence is annotated with a total score of the top5 and topN off-targets and Cas9 | 1. gRNA design 2. off-targeting count 3. score on targeting 4. find Spacer | 4 | User customizable | NGG NAG | [145] |
CHOPCHOP v3 | Web tool for selecting alternative transcription of RNA using CRISPER-CAS13 | gene name, genomic coordinates, or a pasted sequence (including RefSeq and ENSEMBL gene IDs) | 1. gRNA design, Off-targeting 2. GC content (%) 3. number of self-complementary 4. efficiency | - | CRISPR effector (e.g., Cas9, CasX, or Cas13) | NGG | [146] |
E-CRISP | Specific Algorithm used to target any nucleotide sequence ranging from single exons to entire genomes | FASTA | 1. gRNA design (for various targeting purposes) 2. gene annotation filtering 3. off-targeting analysis. 4. image for (genomic context, restriction site, TSS, strop, and start Condon) | - | genomic context (e.g., exons, transcripts, CpG islands) | NGG NAG | [147] |
CRISPy-web | Design sgRNAs | API antiSMASH | gRNA design, Target Site selection | 3 | Cas9 | NGG | [148] |
CRISPR-P 2.0 | Genome editing in plant | Gene name, ID, position, and sequence | 1. on-target score 2. off-target score 3. GC content 4. restriction endonuclease site | - | Cas9 | NGG NAG | [149] |
COSMID | Validation and identification of off-target sequence | FetchGWI search program | Off-target score GC content (%) | 3 | CRISPR Off-target Sites with Mismatches, Insertions, and Deletions | NGG, NAG, NRG | [150] |
WU-CRISPR | Gene editing and detection of CRISPR/Cas9 Knockout | Gene Sequence in FASTA format | 1. gRNA sequence 2. potency score 3. off-target status 4. BLAST alignment 5. coding sequence | - | NGG, | [151] | |
Cas-Designer | Selecting all RGEN targets via Microhomology-predictor | FASTA | 1. RGENs 2. Cas-OFFinder 3. Cas-Designer 4. Cas-Database. | 0-10 | NGG, NRG, NNAGAAW, NNNNGMTT | It depends on the Cas protein. | [152] [153] |
CRISPR MultiTargeter | Web program to detect the High identical site in multiple genes | FASTA | Multiple sequence Alignment | 0-24 | 1. SpCas9 (PAM ‘NGG’), 2. StCas9 (PAM ‘NNAGAAW’), 3. NmCas9 (PAM ‘NNNNGMTT’) | NGG | [154] |