circRNA identification software
| Software | Feature | Website |
|---|---|---|
| Acfs129 | Allows for de novo sequencing, and accurate identification and quantification of circRNAs from single- and double-ended RNA data | code.google.com/p/acfs |
| CIRCfinder22 | Recognizes intron circular RNA | github.com/YangLab/CIRCfinder |
| circRNA_ finder130 | Has high accuracy, independently of gene annotation information | github.com/orzechoj/circRNA_finder.git |
| CIRI-full131 | Recognizes circRNA, assembles the complete nucleotide sequences, and quantifies alternative splicing products of circRNAs | sourceforge.net/projects/ciri-full |
| Circseq_cup132 | Assembles full-length circRNA sequences on the basis of back-splicing RNA-seq and double-terminal RNA-seq data | ibi.zju.edu.cn/bioinplant |
| CircExplorer2133 | Uses integrated multiple alignment algorithms to detect alternative splicing of circRNA, de novo synthesis, and assembly of full-length circRNA transcripts | github.com/YangLab/CIRCexplorer2 |
| CIRI2134 | Based on multiple sub-matching strategies and maximum likelihood estimation models; identifies back-splicing reads and filters false positives from repeated sequences and mapping errors | sourceforge.net/projects/ciri/files/CIRI2 |
| CircView135 | Reveals the structure of circRNA on the basis of species annotation information, allowing users to view the regulatory elements of circRNAs and predict potential functions | gb.whu.edu.cn/CircView |
| CircSplice136 | Specific recognition of alternative splicing events within circRNA, enabling comparison of differences between groups of alternative splicing events of circRNAs | gb.whu.edu.cn/CircSplice |
| DCC137 | Depends on filters and integrated data across repetitive sets to evaluate expression between circRNAs and host genes | github.com/dieterich-lab/DCC |
| find_circ138 | Uses only the fasta sequence of the genome, independently of the gene annotation information | github.com/marvin-jens/find_circ |
| FUCHS139 | On the basis of long read sequencing data, analyzes alternative splicing events in circRNAs, single and double breakpoint events, and the read coverage of circRNAs | github.com/dieterich-lab/FUCHS |
| KNIFE140 | Relies on Bowtie2 for multi-stage correction, combined with read mapping quality and correction quality for static modeling detection of circRNAs | github.com/lindaszabo/KNIFE |
| MapSplice141 | Tag alignment and splice inference (two-step method) | www.netlab.uky.edu/p/bioinfo/MapSplice |
| PRAPI142 | Vector drawing of circRNAs | www.bioinfor.org/bioinfor/tool/PRAPI |
| segemehl143 | Recognizes circRNAs and detects splicing, trans-splicing, and gene fusion events | www.bioinf.uni-leipzig.de/Software/segemehl |
| UROBORUS144 | On the basis of total RNA sequencing data, accurately predicts circRNAs with low expression, but cannot predict circRNAs and circRNAs formed by gene spacers | uroborus.openbioinformatics.org |