New insight into circRNAs: characterization, strategies, and biomedical applications

Feng, Xin-Yi; Zhu, Shun-Xin; Pu, Ke-Jia; Huang, Heng-Jing; Chen, Yue-Qin; Wang, Wen-Tao

doi:10.1186/s40164-023-00451-w

Experimental Hematology & Oncology

Table 1 Bioinformatic tools for circRNAs discovery

From: New insight into circRNAs: characterization, strategies, and biomedical applications

Software	Seq type	Language	Latest update	Download link	Characteristic	Refs.
MapSplice	II	C++	2016	https://github.com/davidroberson/MapSplice2	/	[74]
PcircRNA_finder	II	Python, Perl	2016	http://ibi.zju.edu.cn/bioinplant/tools/manual.htm	Predict circRNAs in plants with frequently used circRNA detect tools	[75]
PredcircRNATool	II	Python	2016	https://sourceforge.net/projects/predicircrnatool/files	Identification of circular RNAs based on conformational and thermodynamic properties in the flanking introns	[108]
CircPro	II	Perl	2017	http://bis.zju.edu.cn/CircPro	Identify the protein-coding potential circRNAs	[198]
CIRI	II	Perl	2017	https://sourceforge.net/projects/ciri	De novo assemble novel circRNA with variable sequencing data	[82]
ACFS	II	Perl, Shell	2017	https://github.com/arthuryxt/acfs	Discovery and annotate circRNA from single-end RNA-seq	[91]
find_circ	II	Python	2017	https://github.com/marvin-jens/find_circ	De novo assemble novel circRNA transcripts and widely used in circbase	[49]
circseq-cup	II	Python	2017	https://github.com/bioinplant/circseq-cup	Identify full-length sequence of circRNAs	[207]
KNIFE	II	Python, Shell, Perl	2017	https://github.com/lindaszabo/KNIFE	Detect and quantify circRNAs from junctional alignments	[208]
PredcircRNA	II	Python	2017	https://github.com/xypan1232/PredcircRNA	Distinguish circRNA from other lncRNAs using multiple kernel learning	[76]
CPSS	II	PHP, Perl, R	2017	http://114.214.166.79/cpss2.0	For small RNA sequencing data analysis	[209]
miARma-seq	II	Perl, Python, R	2018	https://sourceforge.net/projects/miarma	Integration of mRNA, miRNA and circRNA analysis	[210]
CIRI-AS	II	Perl	2018	https://sourceforge.net/projects/ciri	Identify circRNA internal components and alternative splicing events de novo	[211]
hppRNA	II	Perl, R	2018	https://sourceforge.net/projects/hpprna	Analysis circRNA with different core-workflows from a large number of samples	[212]
segemehl	II	C + +	2018	http://www.bioinf.uni-leipzig.de/Software/segemehl	Detect back-splice reads and gene fusion	[83]
STARChip	II	Perl, Shell	2018	https://github.com/LosicLab/STARChip	Output the chimeric reads and discovery fusions circRNAs	[89]
UROBORUS	II	Perl	2018	https://github.com/WGLab/UROBORUS	Suggest detecting circRNAs with low expression levels in RNA-seq	[133]
WebCircRNA	II	Python	2018	https://rth.dk/resources/webcircrna/download	Using machine-learning based method to predict stem cell specific circRNAs	[213]
circRNA_finder	II	Perl, Awk, Shell	2019	https://github.com/orzechoj/circRNA_finder	/	[81]
CircRNAFisher	II	Perl	2019	https://github.com/duolinwang/CircRNAFisher	Identify circRNA de novo	[214]
PRAPI	III	Python	2019	https://pypi.org/project/prapi	One-stop solution of post-transcriptional regulation analysis for Iso-seq, suitable for third generation sequencing	[101]
CircRNAWrap	II	Shell, R	2019	https://github.com/liaoscience/circRNAwrap	Integrate multiple circRNA-detect tools to discovery confidence circRNAs	[85]
RAISE	II	Shell, Perl	2019	https://github.com/liaoscience/RAISE	Integrating detection, quantification and prediction of internal structure	[84]
DeepCirCode	II	Python, R	2019	https://github.com/BioDataLearning/DeepCirCode	Using machine-learning model to predict back-splice sites of circRNA	[77]
ROP	II	Shell, Python	2019	https://github.com/smangul1/rop	Discover the source of all reads with Python2, but it is no longer maintained	[215]
ACValidator	II	Python, Shell	2020	https://github.com/tgen/ACValidator	Assemble circRNA from pseudo-reference file	[216]
CircDBG	II	C + +	2020	https://github.com/lxwgcool/CircDBG	Detect circRNA by de Brujin graph	[217]
CircMarker	II	C + + . Java	2020	https://github.com/lxwgcool/CircMarker	/	[218]
AutoCirc	II	Perl	2020	https://github.com/chanzhou/AutoCirc	Identify back-splice junctions of potential circRNAs from RNA-seq de novo quickly	[24]
Pcirc	II	Python	2020	https://github.com/Lilab-SNNU/Pcirc	Identify plant circRNA with random forest methods	[110]
cirRNAPL	II	Java	2020	http://server.malab.cn/CirRNAPL	Identification of circRNAs based on extreme learning machine	[109]
circDeep	II	Python	2020	https://github.com/UofLBioinformatics/circDeep	Identification of circRNAs with deep learning	[111]
CLEAR	II	Python	2020	https://github.com/YangLab/CLEAR	Combine with ribo-seq & RNA-seq as input, and quantify the expression of circRNAs	[219]
NCLcomparator	II	Roff	2020	https://github.com/TreesLab/NCLcomparator	Detect circRNAs by combined several non-co-linear transcript	[220]
CIRCexplorer	II	Python	2021	https://github.com/YangLab/CIRCexplorer2	De novo assemble novel circRNA with supporting many common aligners	[13]
CIRI-full	II	Perl	2021	https://sourceforge.net/projects/ciri	Reconstruct and quantify full-length circular RNAs from RNA-seq data sets	[134]
CIRI-long	III	Perl	2021	https://sourceforge.net/projects/ciri	Identify circRNA from long-reads sequencing data	[102]
CIRIquant	II	Perl	2021	https://sourceforge.net/projects/ciri	Quantify circRNA expression from RNA-seq data	[221]
CirCompara2	II	Python, R	2021	https://github.com/egaffo/CirComPara2	Integrate multiple circRNA-detect tools to discovery confidence circRNAs	[86]
circAST	II	Python	2021	https://github.com/xiaofengsong/CircAST	Assemble full-length circRNAs and quantification using RNA-Seq data with the back-spliced events	[222]
DCC and CircTest	II	Python	2022	https://github.com/dieterich-lab/DCC	Detect and quantify circRNAs from chimeric reads	[78]
Ularcirc	II	R	2022	https://github.com/VCCRI/Ularcirc	Analysis and visualize the canonical and back-splice junctions, annotate circRNA with overlapping gene information	[80]
NCLscan	II	C + + , Python	2022	https://github.com/TreesLab/NCLscan	Identify both intragenic and intergenic non-co-linear transcript	[205]
circall	II	C + + , R	2022	https://github.com/datngu/Circall	Discovery circRNAs from paired-end RNA-seq	[223]
CYCLeR	II	R	2022	https://github.com/stiv1n/CYCLeR	Reconstruct and quantify circRNAs from RNA-seq datasets accurately	[224]
stackCirRNAPred	II	Python	2022	https://github.com/xwang1427/StackCirRNAPred	Identification of circRNAs based on stacking strategy	[107]
circtools	II	Python, R	2023	https://github.com/dieterich-lab/circtools	Integrate the cumbersome circRNA analysis process of analysis	[225]
circfull	III	Python	2023	https://github.com/yangence/circfull	Detect and quantify full-length circRNA isoforms from circFL-seq	[105]
isocirc	III	Python, R	2023	https://github.com/Xinglab/isocirc	Integrated pipeline to characterize full-length circRNA isoforms using rolling circle amplification	[104]

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ISSN: 2162-3619

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