Table 2 |.
Comparison of in silico off-target site screening tools for CRISPR-Cas9 systems
| Name | Strengths | Weaknesses |
|---|---|---|
| BLAST131 (website, command line) | A time-optimized sequence alignment tool (seeding-based algorithm), bulges allowed | Less accurate (can miss potential off-target sites), limited mismatch numbers, no custom PAM |
| TagScan129 (website, command line) | A time-optimized sequence screening tool for queries <60 bases, web support | Limited mismatch numbers, no custom PAM, no bulges allowed |
| Bowtie61 (command line) | A time-optimized alignment tool for queries <50 bases | Less accurate (can miss potential off-target sites), limited mismatch numbers, no custom PAM, no bulges allowed |
| Bowtie2 (ref. 64) (command line) | A time-optimized alignment tool, bulges allowed | Misses off-target sites with low mismatch numbers80, limited mismatch numbers and no custom PAM |
| CasOT83 (command line) | A sequence screening tool for CRISPR-Cas9 system, custom PAM, user-defined mismatch number in seed/non-seed region, paired-gRNA mode allowed | Time-consuming132, no bulges allowed |
| Cas-OFFinder81 (website, command line) | A commonly used sequence screening tool for CRISPR-Cas systems, web support, custom PAM, user-defined mismatch number, bulges allowed | Can miss potential off-target sites with complex DNA/RNA bulges67, moderate speed132 |
| dsNickFury91(Command line) | A sequence screening tool for CRISPR-Cas9 system, custom PAM, user-defined mismatch number | No bulges allowed |
| FlashFry133 (command line) | A time optimized sequence screening tool for CRISPR-Cas systems, custom PAM, user-defined mismatch number. Good for large datasets | No bulges allowed |
| Crisflash82 (command line) | A sequence screening tool for CRISPR-Cas9 system, custom PAM, user-defined mismatch number, accepts genetic variation data on haplotype level | No bulges allowed |
| CRISPRitz67 (command line) | A time-optimized sequence screening tool for CRISPR-Cas9 system, custom PAM, user-defined mismatch number, bulges allowed, accepts genetic variation data | Cannot process genetic variation data on haplotype level |