# Computational Tools and Resources Supporting CRISPR-Cas Experiments
## 5 Outcomes Analysis  
Another group of algorithms is designed to facilitate the postexperiment (posterior) analysis of the CRISPR-Cas9 edition outcomes, including off-target assessment. Essentially, the postexperiment analysis algorithms enable quantification and visualization of CRISPR-Cas9 outcomes in tabular view with relevant graphs. These algorithms show the frequency of indels and repair types (NHEJ or HDR) simplifying data interpretation. Some of tool such as Tracking of Indels by Decomposition (TIDE) are intended to analyze Sanger sequencing results of the targeted _locus_, providing a comprehensive profile of all insertions and deletions that occurred in a sample [49]. The redesigned version of this tool (TIDER--Tracking of Insertions, Deletions and Recombination events) also enables estimations of the efficacy of templated genome editing and assesses the frequency of HDR events [84]. The advantage of these approaches is that they require basic and easily accessible laboratory equipment and are relatively inexpensive. The other group of programs is concerned with NGS data analysis. Tools such as CRISPRpic, CRIS.py or CrispRV variants provide a command-line interface, which enables a detailed analysis of the results but may be difficult to approach for less experienced users [85; 86; 87; 88]. Therefore, to address this issue, various web-based, command line-less and user-friendly programs for NGS analysis have been developed. CRISPR-Genome Analyzer (CRISPR-GA) uses NGS data to quantify and characterize indels and homologous recombination events at the targeted sites [89]. Its pipeline consists of quality control and alignment of reads, which is subsequently used to compute the editing efficiency and frequency of HDR and NHEJ and to create charts with indel localizations and sizes. Another tool available online is Cas-Analyzer, a JavaScript-based implementation for NGS data analysis [88]. This program provides results similar to those of CRISPR-GA but has one practical advantage: avoiding of a time-consuming step of data upload to a server. The Cas-Analyzer algorithm runs wholly on the side of a web browser, leading to a significant time savings. Moreover, it supports various nucleases used by scientists, including the paired nickases approach. One additional program that facilitates the analysis of sequencing data is CRISPR2, an updated version of the CRISPRoso tool [90; 91]. CRISPR2, aside from performing edit outcome frequency assessment, enables allele-specific quantification of results by aligning reads to multiple reference sequences and computing statistics separately for each allele. Furthermore, CRISPR2 may be very useful for base editing assays due to its detailed analysis of substitutions. The main disadvantage of this tool is the limit of data that can be uploaded for an analysis (up to 100 Mb in one FASTQ file). However, the command line version of CRISPR2 containing additional tools and no data upload limits is available online. We compared the main features of the described tools in Table 2.  
There are also tools dedicated to the analysis of NGS results from pooled screening experiments. Several tools developed for such purposes such as like MAGeCK and BAGEL utilize a command line interface, which may limit their accessibility for less experienced users [93,94]. Newly developed programs that offer web-based and user-friendly interfaces for the deconvolution of pooled screening data, such as CRISPRAnalyzeR, CRISPRcloud2 and PinAPL-Py, are addressed for researchers with zero programming background [95,96,97]. Each of these platforms requires uploading FASTQ files with NGS data and a gRNA library file (predefined gRNA libraries are also provided on websites) to start the workflow. The output of the mentioned tools includes information regarding quality control, detailed statistical analysis and visualization of the data. Moreover, CRISPRAnalyzeR and CRISPRcloud2 offer tutorial videos on their websites, simplifying the usage of these tools.