Table I.
Software for circRNA identification.
| Name | URL | Trait | Refs. |
|---|---|---|---|
| MapSplice | http://www.netlab.uky.edu/p/bioinfo/MapSplice | Two-step method of tag matching and splicing inference | (79) |
| CIRCfinder | https://github.com/YangLab/CIRCfinder | Identification of circRNA in introns | (20) |
| circRNA_finder | https://github.com/orzechoj/circRNA_finder.git | High accuracy. Runs independently of gene annotation information | (29) |
| segemehl | www.bioinf.uni-leipzig.de/Software/segemehl/ | Detects splicing, trans-splicing and gene fusion events | (80) |
| KNIFE | https://github.com/lindaszabo/KNIFE | Static modelling and detection of circRNA. | (81) |
| DCC | https://github.com/dieterich-lab/DCC | Assesses expression between circRNA and host genes | (82) |
| Acfs | https://code.google.com/p/acfs/ | Allows de novo sequencing to accurately identify circRNA and quantify abundance | (83) |
| UROBORUS | http://uroborus.openbioinformatics.org/ | Accurately predicts circRNA with low expression | (40) |
| Circseq_cup | http://ibi.zju.edu.cn/bioinplant/ | Assembly of full-length circRNA sequences | (84) |
| FUCHS | https://github.com/dieterich-lab/FUCHS | Analyses alternative splicing in circRNA, single and double breakpoint events and read coverage of circRNA | (85) |
| CIRI-full | https://sourceforge.net/projects/ciri-full/ | Quantifies alternative splicing products of circRNA | (86) |
| CircExplorer2 | https://github.com/YangLab/CIRCexplorer2 | De novo assembly of full-length circRNA transcripts | (87) |
| CIRI2 | https://sourceforge.net/projects/ciri/files/CIRI2 | Filters false positives from repeated sequences and mapping errors | (88) |
| CircView | http://gb.whu.edu.cn/CircView/ or https://github.com/GeneFeng/CircView | Allows users to view the regulatory elements of circRNA and predict potential function | (89) |
| PRAPI | http://www.bioinfor.org/bioinfor/tool/PRAPI/ | Vector graphics of circRNA | (90) |
| CircSplice | http://gb.whu.edu.cn/CircSplice/ or https://github.com/GeneFeng/CircSplice | Comparison of differences between groups of alternative spliced circRNA | (91) |
circRNA, circular RNA.