|
| Name | Year | Web functions | Web links | Last updated | Refs. |
|
| MapSlice 2 | 2010 | A highly accurate algorithm for alignment of RNA-seq reads to splice junction | http://www.netlab.uky.edu/p/bioinfo/MapSplice2 | 06-13-2016 | [165] |
| Find_circ | 2013 | To detect backspliced sequencing reads, which is an indication of circRNAs in RNA-seq data | https://github.com/marvin-jens/find_circ | 01-06-2017 | [32] |
| CIRCfinder | 2013 | A pipeline to map junction reads for intronic circRNAs | https://github.com/YangLab/CIRCfinder | 03-25-2016 | [166] |
| CircRNA_finder | 2014 | A pipeline to search for circRNAs from RNA-seq data | https://github.com/orzechoj/circRNA_finder | 10-14-2019 | [167] |
| CIRI | 2015 | A de novo circRNA identification tool to detect circRNAs from transcriptome data | https://sourceforge.net/projects/ciri/
https://omictools.com/ciri-tool
https://sourceforge.net/projects/ciri/ | 04-16-2020 | [168, 169] |
| KINFE | 2015 | Known and Novel IsoForm Explorer is a statistically based splicing detection tool for circRNAs and linear isoforms from RNA-seq data | https://github.com/lindaszabo/KNIFE | 07-14-2017 | [45] |
| miARma-seq | 2016 | A comprehensive tool for the identification of miRNAs, mRNAs, and circRNAs | http://miarmaseq.cbbio.es/ (not accessible)
https://sourceforge.net/projects/miarma/ | 06-15-2018 | [170] |
| NCLscan | 2016 | A stepwise alignment strategy to eliminate false calls; to identify both intragenic and intergenic NCL transcripts from paired-end RNA-seq data | https://github.com/TreesLab/NCLscan
ftp://treeslab1.genomics.sinica.edu.tw/NCLscan | 05-21-2020 | [125] |
| UROBORUS | 2016 | A computational pipeline to detect circRNAs in total RNA-seq data | http://uroborus.openbioinformatics.org/ (NA) | NA | [171] |
| deepBase v2.0 | 2016 | To decode evolution, expression patterns, and functions of diverse ncRNAs (incl. circRNAs) across 19 species | http://biocenter.sysu.edu.cn/deepBase/ (NA)
https://omictools.com/deepbase-tool | NA | [172] |
| Acfs | 2016 | A pipeline for de novo circRNA identification, allowing the discovery of circRNAs from RNA-seq data | https://github.com/arthuryxt/acfs | 02-16-2017 | [173] |
| pcircRNA_finder | 2016 | A pipeline for the prediction of plant circRNAs | http://ibi.zju.edu.cn/bioinplant/tools/manual.htm | NA | [174] |
| PTESFinder | 2016 | A computational pipeline for identifying posttranscriptional exon shuffling events from HTS data | https://sourceforge.net/projects/ptesfinder-v1/ | 09-04-2017 | [126] |
| CirComPara | 2017 | A multimethod comparative bioinformatics pipeline to detect and study circRNAs from RNA-seq data | https://github.com/egaffo/CirComPara | 12-21-2016 | [172] |
| RAISE | 2017 | A pipeline for circRNA backsplice sites and used for identification, quantification of abundance, and prediction of their internal structure using RNA-seq data | https://github.com/liaoscience/RAISE | 03-13-2017 | [175] |
| CircPro | 2017 | An integrated tool for identification of circRNAs with protein-coding potential | http://bis.zju.edu.cn/CircPro/ | NA | [176] |
| AutoCirc | 2017 | A pipeline that allows definition of m6A circRNAs with cell-type-specific expression | https://github.com/chanzhou/AutoCirc | 04-08-2020 | [177] |
| PRAPI | 2018 | A pipeline to analyze differential expression of circRNAs | http://forestry.fafu.edu.cn/tool/PRAPI/ | 12-05-2019 | [178] |
| hppRNA | 2018 | A snakemake-based RNA-seq pipeline to analyze circRNAs | https://sourceforge.net/projects/hpprna/ | 12/18-2018 | [179] |
| NetMiner | 2018 | A pipeline to construct a high-quality RNA-seq-based gene coexpression network and to predict biological functions of novel circRNAs | https://github.com/czllab/NetMiner | 11-06-2017 | [180] |
| Docker4Circ | 2019 | A comprehensive analysis of circRNAs in human and model organisms, including circRNA prediction, classification, and annotation | https://github.com/kendomaniac/docker4seq
https://github.com/mbeccuti/4SeqGUI | 02-20-2019
07-21-2017 | [181] |
| circtools | 2019 | A Python-based framework for circRNA-related tools that use a single command to unify different functionalities | https://github.com/dieterich-lab/circtools | 02-27-2019 | [182] |
| CircRNAFisher | 2019 | For de novo genome-wide circRNA identification and annotation | https://github.com/duolinwang/CircRNAFisher.
Note: bowtie2 is required.
http://bowtie-bio.sourceforge.net/bowtie2 | 07-06-2019 | [183] |
| CIRCexplorer3 | 2019 | Analysis of circRNAs and linear RNAs from rRNA-depleted RNA-seq data | https://github.com/YangLab/CLEAR
https://github.com/YangLab/CIRCexplorer2 | 01-28-2020 | [121, 184] |
| circCode | 2019 | A Python-based pipeline to identify the coding ability of circRNAs | https://github.com/PSSUN/CircCode | 05-19-2020 | [185] |
| circMiner | 2020 | A fast and sensitive tool to detect circRNAs from RNA-seq data | https://github.com/vpc-ccg/circminer | 05-01-2020 | [186] |
| circDeep | 2020 | A deep learning approach for circRNA classification from long noncoding RNAs | https://github.com/UofLBioinformatics/circDeep | 01-28-2018 | [187] |
| circDBG | 2020 | circRNA detection from high-throughput sequence data with de Bruijn’s graph | https://github.com/lxwgcool/CircDBG | 03-06-2020 | [188] |
| CircParser | 2020 | A Unix/Linux-based pipeline to predict host gene circRNAs | https://github.com/SharkoTools/CircParser | 03-27-2020 | [189] |
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