From: CRISPR/Cas9: the Jedi against the dark empire of diseases
Tool | Website | Purpose | Input | Output | Available genomes | Pros | Cons | Reference |
---|---|---|---|---|---|---|---|---|
Atum | Candidate gRNA | DNA sequence, (max 10,000 bp) gene name, genomic region | Candidate guidesequences and off target loci | 5 | Uses ATUM scoring to minimize off-targets/all in one nickase ninja | Not free of cost | N/A | |
Benchling | Candidate gRNA | DNA sequence/gene name | Candidate guidesequences and off target loci | 5 | Free of cost |  | N/A | |
CRISPR design | Used to find target sequences for a sequence or seuqnces (batch mode), also provides in depth on/off target information | DNA sequence/FASTA files single or batch mode | Candidate guide sequences and off target loci | 16 | Helpful to generate many candidates with on/off information | Only handles short sequences up to23–500 bp/slow to use/no efficacy merit/does not indicate identity of mismatches | [39] | |
CHOPCHOP | To find target sequences for a single sequence/gene/transcript | DNA sequence/gene name/genome location | Candidate guide sequences and off target loci, | 23 | Good to generate multiple guides for a single target, free of cost | No on-target efficacy | [40] | |
Cas off finder | Provides information about OTs without limiting the PAM or number of mismatch bases | sgRNA | Off target loci for guide sequences | 20 | Free of cost/easy to use | Does not give indication if OTs are in coding sequences | [41] | |
Fly CRISPR | Candidiate gRNA, software provides maximum stringency-(uses strict algorithm based on OT cleavage in cells lines) and minimum stringency; off target cleavage effects observed | DNA sequence | Candidate guidesequences and off target loci, | 18 | Free of cost | Slow to use | [42] | |
E-CRISP | Finds target sequences for a single gene or sequence | DNA sequence/gene symbol | Candidate guide sequences and off target loci, | 30 | Free of cost | Numerous options maybe confusing/no account for identity of mismatches | [43] | |
Cas OT | To find potential off targets in any genome | FASTA files | sgRNA and OT sites | User input | Free of cost/ First tool that identifies off-targetes in a user specified genome | No account for identitiy of mismatches | N/A | |
CRISPR ERA | Used for genome wide screening based on CRISPR, CRISPRi and CRISPRa | DNA sequence, gene name or TSS location | Candidate guide sequences and distances to TSS | 9 | Free of cost/can also be used for genome imaging and CRISPR synthetic circuit design |  | [44] | |
CCTop | It helps in identifying and ranking all sgRNA targets sites according to off target quality | DNA sequence/FASTA file single/batch/ sequences 23 to 500 bp | Scores OTs and also ranks sgRNA by OTs | 45 | Free of cost/easy to use | No on–target efficacy prediction | [45] | |
WU-CRISPR | Potential candidate gRNA | DNA sequence/gene symbol | sgRNA list ranked by efficacy score | 2 (Human and mouse) | Free of cost/easy to use | No account of identity of mismatches | [46] | |
GTscan | Used to find target sequences and OTs for a single sequence | DNA sequence/FASTA file | SgRNA, genomic sites with 0 to 3 mismatches | 51 | Free of cost/easy to use | Trouble in finding exact matches in genome | [47] | |
CRISPR direct | To find target sequences for a single transcript/sequence | DNA sequence/genome location/transcript | Target sequence and position | 20 | Free of cost/rapid visual display of target sequence and OT information | No on-target efficacy | [48] | |
COD | Used to find target sequences for an input sequence | DNA sequence up to 400 bp | Gene bank file/CSC file/ OT scoring | 27 | Free of cost/easy to use/ OT scoring | Slow to use/no on-taget prediction | N/A | |
sgRNA scorer 2.0 | Used to find target sequences/OT using Casfinder | DNA sequence/FASTA files upto10 kb | Target sequence with activity score | 14 | Free of cost/ allows to identify target sites for any CRISPR system | Slow to use/OT prediction does not account identity | N/A | |
CRISPOR | To find candidate guide sequences | DNA sequence 1000 bp | Guide sequence with specificity score/guides for OTs | 146 | Free of cost | N/A | [49] |