Table 5 List of main Bioinformatics tools with their features and types of Cas proteins

CRISPResso2

Human and mouse

Cas9 Cpf1

Amplicon sequencing and its interpretation for genome editing

http://crispresso2.pinellolab.org/submission

[187]

Cas-Analyzer (CRISPR-GA)

Human, mouse, rat, drosophila, zebrafish

NmCas9, SpCas9, SaCas9, StCas9, AsCpf1/LbCpf1

Editing genomes and creating synthetic nucleases (programmable nucleases)

https://crispr-ga.net/

[188]

CRISPOR

Human, Arthropoda

Cas9 orthologues, Cas variants

Primer sets, genomic location of targets, and numerous predictive models

http://crispor.tefor.net/

[189]

TIDE/TIDER

–

SpCas9, SaCas9, St1Cas9, NmCas9, AsCpf1, FnCpf1, LbCpf1

Large-scale induced mutations in the editing site are identified with a custom deconstruction approach

http://shinyapps.datacurators.nl/tider/

[190]

CHOPCHOP

Human, mouse, zebrafish, bacteria

Cas9, Cas12, Cas13, TALEN

Providing multiple predictive models; visualizing genomic location of targets and genes; and providing primers

https://chopchop.cbu.uib.no/

[191]

CRISPR RGEN Tools

Human

Cas9

Microhomology-predictor predicts out-of-frame scores, predicts probable off-target numbers, and can be used independently

http://www.rgenome.net/

[192]

E-CRISP

Human

SpCas9

Genome-scale library construction in a practical manner; freely available and regularly updated

http://www.e-crisp.org/E-CRISP/

[193]

CRISPRscan

Human

Cas9, Cas12

Coding-gene sgRNA design and genome browser tracks

https://www.crisprscan.org/

[194]

CCTop

Human, mouse model

Cas9

Easy to use, highly customizable, single and multiple query searching; identifying mismatches; estimating off-target impacts; sgRNA efficiency prediction

https://cctop.cos.uni-heidelberg.de:8043/

[195]

CRISTA

–

SpCas9

Offering a machine learning framework for identifying false positives and prioritizing targets, which is more precise than existing methods

https://crista.tau.ac.il/

[196]

DeepCRISPR

Human

SpCas9

Predicting off-target effects by factoring in epigenetic data

https://github.com/bm2-lab/DeepCRISPR

[197]

WU-CRISPR

Human, mouse

SpCas9

Offering an ML algorithm that has been highest prediction scores

https://bio.tools/wu-crispr

[198]

CRISPRz

Zebrafish, human, mouse

SpCas9

Specific for a wide range of species and cell lines

https://research.nhgri.nih.gov/CRISPRz/?mode=search

[199]

AsCRISPR

Human, mouse

SpCas9, AaCas12b, AsCpf1, CasX

Creating sgRNAs for genomic sites with specified alleles

https://bio.tools/AsCRISPR

[200]

CRISPRlnc

Human

SpCas9

Making a validated sgRNA database for lncRNAs downloadable

http://www.crisprlnc.org/

[201]