Table 1.
Selected circRNA identification tools
| Tool name | ST | TT | IT | QS | ATMR | AC | PL | LU | CV | Platform | Link | Ref |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CIRCexplorer | PE, SE | De novo; annotation | pip, Conda, Docker | YES | STAR, BWA | BSJ | Python | 2019 | v2.3.8 | Unix/Linux | https://github.com/YangLab/CIRCexplorer2 | [24, 46] |
| CircPro | PE, SE | De novo; annotation | MID | YES | BWA (CIRI2) | BSJ | Perl | 2017 | — | Unix/Linux | http://bis.zju.edu.cn/CircPro | [73] |
| MapSplice | PE, SE | De novo; annotation | Conda | YES | Bowtie | BSJ | Python | 2016 | v2.2.1 | Unix/Linux | http://www.netlab.uky.edu/p/bioinfo/MapSplice2 | [48] |
| circRNA_finder | PE, SE | De novo | MID | YES | STAR | BSJ | Perl, AWK | 2019 | v1.2 | Unix/Linux | https://github.com/orzechoj/circRNA_finder | [51] |
| CircRNAFisher | PE | De novo | MID | YES | Bowtie2 | BSJ | Perl | 2019 | v0.1 | Unix/Linux | https://github.com/duolinwang/CircRNAFisher | [65] |
| miARma | PE, SE | De novo | Docker, Virtualbox image | YES | BWA (CIRI) | BSJ | Perl, Python, R | 2018 | v1.7.5 | Unix/Linux, Windows | https://sourceforge.net/projects/miarma/ | [67] |
| CIRI | PE, SE | De novo | MID | YES | BWA | BSJ | Perl | 2017 | v2.0.6 | Unix/Linux | https://sourceforge.net/projects/ciri/ | [43–45] |
| ACFS | PE, SE | De novo | MID | YES | BWA, BLAT | BSJ | Perl | 2016 | v2 | Unix/Linux | https://github.com/arthuryxt/acfs | [59] |
| find_circ | SE | De novo | MID | YES | Bowtie2 | BSJ | Python | 2015 | v1.2 | Unix/Linux | https://github.com/marvin-jens/find_circ | [9] |
| ACValidator | PE, SE | Annotation | pip, MID | NULL | BWA，Bowtie2 | BSJ | Python, Shell | 2019 | v1.0 | Unix/Linux | https://github.com/tgen/ACValidator | [56] |
| ANNOgesic | PE, SE | Annotation | pip3, Docker | NULL | segemehl | BSJ | Python | 2019 | v1.0.8 | Unix/Linux | https://github.com/Sung-Huan/ANNOgesic | [63] |
| BIQ | PE, SE | Annotation | nmp | NULL | k-mer (no need aligner) | BSJ | C++, Perl, JavaScript | 2019 | v0.2.0 | Unix/Linux, Windows | https://github.com/pmenzel/biq | [58] |
| CircDBG | PE | Annotation | CR | NULL | k-mer (no need aligner) | BSJ | C++ | 2019 | — | Unix/Linux | https://github.com/lxwgcool/CircDBG | [54] |
| CircMarker | PE, SE | Annotation | CR, MID | NULL | k-mer (no need aligner) | BSJ | C++ | 2019 | — | Unix/Linux | https://github.com/lxwgcool/CircMarker | [53] |
| circtools | PE, SE | Annotation | pip3, SS, Bioconductor | YES | DCC, FUCHS | BSJ | Python, R | 2019 | Release 1.1.0.8 | Unix/Linux | https://github.com/dieterich-lab/circtools | [69] |
| DCC and CircTest | PE, SE | Annotation | SS | YES | STAR | BSJ | Python, R | 2019 | — | Unix/Linux | https://github.com/dieterich-lab/ | [47] |
| NCLcomparator | PE, SE | Annotation | MID | YES | STAR, BLAT | BSJ | Shell | 2019 | v1.0.0 | Unix/Linux | https://github.com/TreesLab/NCLcomparator | [55] |
| PRAPI | PE, SE | Annotation | MID, pip | YES | CIRIexplorer | BSJ | Python, R | 2019 | V6.2.0 | Unix/Linux | http://www.bioinfor.org/bioinfor/tool/PRAPI/ | [72] |
| PTESFinder | PE, SE | Annotation | MID | YES | Bowtie | BSJ | Java, Shell | 2019 | v1 | Unix/Linux | https://sourceforge.net/projects/ptesfinder-v1/ | [52] |
| Ularcirc | PE, SE | Annotation | devtools, Conda, Bioconductor | YES | STAR | BSJ | R | 2019 | v1.3.24 | Unix/Linux, Windows | https://github.com/VCCRI/Ularcirc | [49] |
| AutoCirc | PE, SE | Annotation | MID | YES | Bowtie2 | BSJ | C++, Perl | 2018 | v1.3 | Unix/Linux | https://github.com/chanzhou/AutoCirc | [64] |
| hppRNA | PE, SE | Annotation | SS | YES | STAR (DCC and CircTest) | BSJ | Perl, R | 2018 | v1.3.7 | Unix/Linux, Windows | https://sourceforge.net/projects/hpprna/ | [66] |
| Identify circularRNA reads | PE | Annotation | MID | YES | STAR | BSJ | Perl | 2018 | - | Unix/Linux, Windows | https://bitbucket.org/snippets/MSmid/Le949d/identify-circularrna-reads | [57] |
| ROP | PE, SE | Annotation | SS | YES | TopHat-Fusion, CIRCexplorer2 | BSJ | Shell | 2018 | v1.1.2 | Unix/Linux | https://github.com/smangul1/rop | [61] |
| segemehl | PE, SE | Annotation | CR, Conda | NULL | segemehl | BSJ | C++ | 2018 | Release 0.3.4 | Unix/Linux | https://www.bioinf.uni-leipzig.de/Software/segemehl/ | [40, 41] |
| STARChip | PE, SE | Annotation | MID | YES | STAR | BSJ | Perl, R, Shell | 2018 | v1.3e | Unix/Linux | https://github.com/LosicLab/STARChip | [62] |
| UROBORUS | PE, SE | Annotation | MID | YES | Bowtie | BSJ | Perl | 2018 | v2.0.6 | Unix/Linux | https://github.com/WGLab/UROBORUS | [50] |
| circScan | PE, SE | Annotation | CR | YES | Bowtie2 | BSJ | C++, Perl | 2017 | v0.1 | Unix/Linux | https://github.com/sysu-software/circscan | [70] |
| circTools (starBase) | PE, SE | Annotation | CR, MID | NULL | Bowtie2 | BSJ | C++ | 2017 | v0.1 | Unix/Linux | http://starbase.sysu.edu.cn/starbase2/circTools.php | [71] |
| circseq-cup | PE, SE | Annotation | MID | NULL | TopHat, STAR, segemehl | BSJ | Perl, Python | 2016 | v1.0 | Unix/Linux | https://github.com/bioinplant/circseq-cup/ | [68] |
| exceRpt | PE, SE | Annotation | Docker | YES | STAR, Bowtie2 | BSJ | R, Sell, Perl | 2016 | v4.3.2 | Unix/Linux, Windows | http://github.gersteinlab.org/exceRpt/ | [97] |
| KNIFE | PE, SE | Annotation | MID | YES | Bowtie2, Bowtie | BSJ | Python, R, Perl, Shell | 2016 | v1.5 | Unix/Linux | https://github.com/lindaszabo/KNIFE | [39] |
| NCLscan | PE | Annotation | CR | YES | BWA, BLAT | BSJ | Python, C++ | 2016 | v1.6 | Unix/Linux | https://github.com/TreesLab/NCLscan | [60] |
| CircularRNAPipeline | PE, SE | Annotation | MID | YES | CIRCExplorer, TopHat-Fusion | BSJ | Python | 2015 | — | Unix/Linux | https://github.com/huboqiang/TanglabCircularRNAPipeline | [75, 76] |
| circ_battle | PE, SE | De novo, annotation | — | YES | — | IPA | — | 2018 | — | Web-based | http://174.138.53.214:3838/circ_battle/ | [77] |
| CirComPara | PE, SE | Annotation | SS, Docker | YES | — | IPA | Python, R | 2019 | v1.0 | Unix/Linux | http://github.com/egaffo/CirComPara | [79] |
| CircRNAwrap | PE, SE | Annotation | MID | YES | — | IPA | Perl, Shell, R | 2019 | — | Unix/Linux | https://github.com/liaoscience/circRNAwrap | [82] |
| RAISE | PE, SE | Annotation | MID | YES | — | IPA | Shell | 2017 | — | Unix/Linux | https://github.com/liaoscience/RAISE | [80] |
| PcircRNA_finder | PE, SE | Annotation | MID | YES | — | IPA | Perl, Python | 2016 | — | Unix/Linux | http://ibi.zju.edu.cn/bioinplant/tools/manual.htm | [81] |
| DeepCirCode | — | De novo; annotation | devtools | NULL | — | ML | R | 2019 | v1.0.0 | Unix/Linux, Windows | https://github.com/BioDataLearning/DeepCirCode | [86] |
| WebCircRNA | — | De novo; annotation | — | NULL | — | ML | Python | 2018 | — | Web-based, Unix/Linux | https://rth.dk/resources/webcircrna/ | [84] |
| PredcircRNA | — | De novo; annotation | MID | NULL | — | ML | Python | 2017 | — | Unix/Linux | https://github.com/xypan1232/PredcircRNA | [83] |
| PredicircRNATool | — | annotation | MID | NULL | — | ML | MATLAB | 2016 | — | Unix/Linux, Windows | https://sourceforge.net/projects/predicircrnatool/files/ | [85] |
| CPSS | PE, SE | annotation | — | YES | — | NULL | Perl, PHP, R | 2017 | v2.0 | Web-based | http://114.214.166.79/cpss2.0/ | [74] |
Header abbreviations: AC, algorithm category; ST, sequencing type; TT, tools type; IT, installation type; LU, last update; CV, current version; Ref, reference; QS, quantification support; ATMR, aligner or tools or method required; PL, programming language.
Column descriptions: ‘Tool Name’ is the name of related tools. ‘ST’ column describes the tool supported sequencing type. ‘TT’ column describes the type of the tool. If the tool needs a gene annotation file, the tool is labeled with ‘annotation’, otherwise, it is labeled with ‘De novo’. ‘IT’ column describes the tool supported installation methods, such as Docker image installation and Conda installation. ‘QS’ column describes whether the tool can be used to measure the quantification of circRNAs. ‘ATMR’ column describes the aligner or method of the tool. ‘AC’ column describes the algorithm of the tool. ‘PL’ column describes which programming language is used to develop the tool. ‘LU’ column describes the latest update time of the tool. ‘CV’ column describes the current version of the tool. ‘Platform’ column describes the tool supported platforms. ‘Link’ column provides the homepage of the tool or the link which gives more detailed information about the tool. ‘Ref’ column provides the related publications.
Other abbreviations: BSJ, back-splice-junction-based method; IPA, integrated prediction algorithms; ML, machine learning-based method; PE, paired-end; SE, single-end; MID, manually install dependencies; CR, compile required (make command); SS, setup script is available.