TABLE 1.
Tools and software packages related to CRISPR systems.
| Name | Main functionality | Input | Cell type | Interface | Year | Source |
|---|---|---|---|---|---|---|
| CRISPRidentify Mitrofanov et al. (2021)* | It detects All possible CRISPR arrays | Genome sequences | Bacteria and archaeal | Standalone application | 2021 | https://github.com/BackofenLab/CRISPRidentify |
| CRISPRloci Alkhnbashi et al. (2021)* | Definition of CRISPR leaders for each locus; Prediction of all CRISPR arrays in the correct orientation; annotation of Cas genes and associated information, include the Cas subtypes | Protein, genomic DNA, CRISPR repeats or viral sequences are accepted | Bacteria, archaeal and viral | Webserver and standalone versions (Python, Perl and Java) | 2021 | Webserver: https://rna.informatik.unifreiburg.deCRISPRloci |
| Standalone version: https://github.com/BackofenLab/CRISPRloci | ||||||
| ANNOgesic Yu et al. (2018) | It can detect several genomic features, including genes, CDSs, tRNAs, rRNAs, TSSs, PSs, transcripts, terminators, UTRs, sRNAs, sORFs, circular RNAs, CRISPR-related RNAs, riboswitches, and RNA-thermometers | RNA-seg | Bacterial and archaeal genome | Command-line (Python) | 2018 | The software: https://pypi.org/project/ANNOge/ https://hub.docker.com/r/silasysh/annogesic/Documentation: http://annogesic.readthed.ocs.io/ |
| CRISPR-DAV Wang et al. (2017) | A pipeline to analyze the CRISPR NGS data in a high-throughput manner. Output: read counts in various stages; read depths and indel frequencies in amplicon; counts and percentages of indel reads; frequencies of allele, SNP and HDR. | Files that describe software paths, parameters, mplicon, CRISPR sites, and FASTQ sources | Any selected genome | Command line Interface (Perl and R) | 2017 | https://github.com/pinetree1/crispr-dav.git and https://hub.docker.com/r/pinetree1/crispr-dav |
| Cas-analyzer Park et al. (2017)* | It is an NGS data analyzer. It categorizes and sorts the results. The position and size of insertions or deletions are depicted as interactive graphs | Deep sequencing data | Any selected genome | Web user interface (JavaScript) | 2017 | http://www.rgenome.net/cas-analyzer/ |
| CRISPRAnalyzeR Winter et al. (2017)* | An application to analyze, document, and explore pooled CRISR/Cas9 screens. Reagent phenotypes such as efficiency scores and predicted genomic binding sites are displayed | An sgRNA library or screening data | Any selected genome | Open-source web or standalone application | 2017 | http://www.crispranalyzer.org |
| source code at: http://www.github.com/boutroslab/CRISPRAnalyzeR | ||||||
| CRISPRcloud Jeong et al. (2017) | An application to extract, cluster, and analyze raw next-generation sequencing files derived from pooled screening experiments | sgRNA read counts data | Human and mouse | Cloud-based web application | 2017 | http://crispr.nrihub.org |
| CRISPRdigger Ge et al. (2016) | can Discover Direct Repeats (DRs) for CRISPRs and achieve a higher accuracy for a query genome | A genome sequence | Any selected genome | Command line application | 2016 | http://www.healthinformaticslab.org/supp/ |
| BATCH-GE Boel et al. (2016) | It detects and reports indel mutations and other precise genome editing events and calculates the corresponding mutagenesis efficiencies | NGS-derived sequencing data, DNA of interest | Any selected genome | Command line application | 2016 | https://github.com/WouterSteyaert/BATCH-GE.git |
| CRISPRleader O’Brien and BaileyGT-Scan. (2014) | It detects leader sequences and shows full annotation of the CRISPR array and its strand orientation as well as conserved core leader boundaries | Genome sequence | Archaea and bacteria | Command line application (HTML pages) | 2016 | http://www.bioinf.unifreiburg.de/Software/CRISPRleader/ |
| CRISPRDetect Biswas et al. (2016)* | It enables accurate identification of CRISPR arrays in genomes and their direction, repeat spacer boundaries, substitutions, insertions or deletions in repeats and spacers. It lists Cas genes that are annotated in the genome | Four inputs: genomic sequence, word size, min of word repeat, and max gap between repeats | Archaea and bacteria | Web application and command line (PERL) | 2016 | http://bioanalysis.otago.ac.nz/CRISPRDetect/ |
| CRISPR-GA Güell et al. (2014) | It estimates the HR, NHEJ, and a complete report of the location and characteristics of the indels | The genomic region | Any selected genome | Web user interface (implemented in R) | 2014 | http://crispr-ga.net. Documentation at: http://crispr-ga.net/documentation.html |
| Crass Skennerton et al. (2013) | It identifies and reconstructs CRISPR loci from raw metagenomic data without the need for assembly or prior knowledge of CRISPR in the data set. | Raw file in FASTA or FASTq format | All genome | Command line interface | 2013 | http://bioinformatics.ninja/crass |