From: New insight into circRNAs: characterization, strategies, and biomedical applications
Software | Seq type | Language | Latest update | Download link | Characteristic | Refs. |
---|---|---|---|---|---|---|
MapSplice | II | C++  | 2016 | / | [74] | |
PcircRNA_finder | II | Python, Perl | 2016 | Predict circRNAs in plants with frequently used circRNA detect tools | [75] | |
PredcircRNATool | II | Python | 2016 | Identification of circular RNAs based on conformational and thermodynamic properties in the flanking introns | [108] | |
CircPro | II | Perl | 2017 | Identify the protein-coding potential circRNAs | [198] | |
CIRI | II | Perl | 2017 | De novo assemble novel circRNA with variable sequencing data | [82] | |
ACFS | II | Perl, Shell | 2017 | Discovery and annotate circRNA from single-end RNA-seq | [91] | |
find_circ | II | Python | 2017 | De novo assemble novel circRNA transcripts and widely used in circbase | [49] | |
circseq-cup | II | Python | 2017 | Identify full-length sequence of circRNAs | [207] | |
KNIFE | II | Python, Shell, Perl | 2017 | Detect and quantify circRNAs from junctional alignments | [208] | |
PredcircRNA | II | Python | 2017 | Distinguish circRNA from other lncRNAs using multiple kernel learning | [76] | |
CPSS | II | PHP, Perl, R | 2017 | For small RNA sequencing data analysis | [209] | |
miARma-seq | II | Perl, Python, R | 2018 | Integration of mRNA, miRNA and circRNA analysis | [210] | |
CIRI-AS | II | Perl | 2018 | Identify circRNA internal components and alternative splicing events de novo | [211] | |
hppRNA | II | Perl, R | 2018 | Analysis circRNA with different core-workflows from a large number of samples | [212] | |
segemehl | II | C +  +  | 2018 | Detect back-splice reads and gene fusion | [83] | |
STARChip | II | Perl, Shell | 2018 | Output the chimeric reads and discovery fusions circRNAs | [89] | |
UROBORUS | II | Perl | 2018 | Suggest detecting circRNAs with low expression levels in RNA-seq | [133] | |
WebCircRNA | II | Python | 2018 | Using machine-learning based method to predict stem cell specific circRNAs | [213] | |
circRNA_finder | II | Perl, Awk, Shell | 2019 | / | [81] | |
CircRNAFisher | II | Perl | 2019 | Identify circRNA de novo | [214] | |
PRAPI | III | Python | 2019 | One-stop solution of post-transcriptional regulation analysis for Iso-seq, suitable for third generation sequencing | [101] | |
CircRNAWrap | II | Shell, R | 2019 | Integrate multiple circRNA-detect tools to discovery confidence circRNAs | [85] | |
RAISE | II | Shell, Perl | 2019 | Integrating detection, quantification and prediction of internal structure | [84] | |
DeepCirCode | II | Python, R | 2019 | Using machine-learning model to predict back-splice sites of circRNA | [77] | |
ROP | II | Shell, Python | 2019 | Discover the source of all reads with Python2, but it is no longer maintained | [215] | |
ACValidator | II | Python, Shell | 2020 | Assemble circRNA from pseudo-reference file | [216] | |
CircDBG | II | C +  +  | 2020 | Detect circRNA by de Brujin graph | [217] | |
CircMarker | II | C +  + . Java | 2020 | / | [218] | |
AutoCirc | II | Perl | 2020 | Identify back-splice junctions of potential circRNAs from RNA-seq de novo quickly | [24] | |
Pcirc | II | Python | 2020 | Identify plant circRNA with random forest methods | [110] | |
cirRNAPL | II | Java | 2020 | Identification of circRNAs based on extreme learning machine | [109] | |
circDeep | II | Python | 2020 | Identification of circRNAs with deep learning | [111] | |
CLEAR | II | Python | 2020 | Combine with ribo-seq & RNA-seq as input, and quantify the expression of circRNAs | [219] | |
NCLcomparator | II | Roff | 2020 | Detect circRNAs by combined several non-co-linear transcript | [220] | |
CIRCexplorer | II | Python | 2021 | De novo assemble novel circRNA with supporting many common aligners | [13] | |
CIRI-full | II | Perl | 2021 | Reconstruct and quantify full-length circular RNAs from RNA-seq data sets | [134] | |
CIRI-long | III | Perl | 2021 | Identify circRNA from long-reads sequencing data | [102] | |
CIRIquant | II | Perl | 2021 | Quantify circRNA expression from RNA-seq data | [221] | |
CirCompara2 | II | Python, R | 2021 | Integrate multiple circRNA-detect tools to discovery confidence circRNAs | [86] | |
circAST | II | Python | 2021 | Assemble full-length circRNAs and quantification using RNA-Seq data with the back-spliced events | [222] | |
DCC and CircTest | II | Python | 2022 | Detect and quantify circRNAs from chimeric reads | [78] | |
Ularcirc | II | R | 2022 | Analysis and visualize the canonical and back-splice junctions, annotate circRNA with overlapping gene information | [80] | |
NCLscan | II | C +  + , Python | 2022 | Identify both intragenic and intergenic non-co-linear transcript | [205] | |
circall | II | C +  + , R | 2022 | Discovery circRNAs from paired-end RNA-seq | [223] | |
CYCLeR | II | R | 2022 | Reconstruct and quantify circRNAs from RNA-seq datasets accurately | [224] | |
stackCirRNAPred | II | Python | 2022 | Identification of circRNAs based on stacking strategy | [107] | |
circtools | II | Python, R | 2023 | Integrate the cumbersome circRNA analysis process of analysis | [225] | |
circfull | III | Python | 2023 | Detect and quantify full-length circRNA isoforms from circFL-seq | [105] | |
isocirc | III | Python, R | 2023 | Integrated pipeline to characterize full-length circRNA isoforms using rolling circle amplification | [104] |