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CIRI specifications


Unique identifier OMICS_09198
Alternative name CIRI2
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTA, SAM, GFT
Operating system Unix/Linux, Mac OS
Programming languages Perl
Computer skills Advanced
Version 2.0.6
Stability Stable
Maintained Yes


No version available



  • person_outline Fangqing Zhao

Publications for CIRI

CIRI citations


Circular RNA expression and regulatory network prediction in posterior cingulate astrocytes in elderly subjects

BMC Genomics
PMCID: 5941680
PMID: 29739336
DOI: 10.1186/s12864-018-4670-5

[…] 85,000,000 reads were sequenced for each sample, with an average mapping percentage of 70.8. Using FASTQ files generated from sequencing, we ran four circRNA prediction algorithms - CIRCexplorer [], CIRI [], find_circ [], and KNIFE [], and detected a total of 4438 unique circRNAs with at least two supporting junction reads (Additional file : Table S1). Among the detected circRNA candidates, a tot […]


Improved circRNA Identification by Combining Prediction Algorithms

PMCID: 5844931
PMID: 29556495
DOI: 10.3389/fcell.2018.00020
call_split See protocol

[…] ercer et al. () 2- and 0.7-fold cutoffs were used. Furthermore, to enable comparison between algorithms, the starting coordinate was converted to 0-based for certain algorithms (ACFS, circRNA_finder, CIRI, CIRI2, DCC, and MapSplice). For de novo prediction, the algorithms with mandatory gene-annotation input (CIRCexplorer2, KNIFE and MapSplice) were provided a mock annotation file to eliminate any […]


Genome Wide Identification of circRNAs in Pathogenic Basidiomycetous Yeast Cryptococcus neoformans Suggests Conserved circRNA Host Genes over Kingdoms

PMCID: 5867839
PMID: 29495353
DOI: 10.3390/genes9030118

[…] ming adaptors and filtering low-quality reads, we obtained 39.28 million clean reads (). Clean reads were then mapped to the C. neoformans JEC21 genome by BWA software. The mapped reads were input to CIRI, a published circRNA identifier, to identify the candidates of circRNAs. To reduce false-positive candidates, the circRNAs that had more than one back-splicing junction read were considered. Afte […]


Recently Evolved Tumor Suppressor Transcript TP73 AS1 Functions as Sponge of Human Specific miR 941

Mol Biol Evol
PMCID: 5913670
PMID: 29474580
DOI: 10.1093/molbev/msy022

[…] cRNA transcripts were identified based on 58 circRNA data including four human PFC samples generated in this study and 54 published circRNA sequencing data (, online). CircRNAs were identified using CIRI (). Briefly, the raw circRNA sequencing data were mapped to the human genome (hg19) using BWA-MEM () with default parameters except “-T 19” (filters out alignments with score < 19), as recommende […]


Luminal breast cancer specific circular RNAs uncovered by a novel tool for data analysis

PMCID: 5865691
PMID: 29581865
DOI: 10.18632/oncotarget.24522
call_split See protocol

[…] nditions: i) hormone-deprived (HD) media ii) HD+ 17β-estradiol (6h) iii) medium added of FBS 10% iv) double-stranded RNA complementary to ESR1 mRNA (siRNA) (48h). Raw data are deposited at GSE101410. CIRI v. 1.2 [] circRNA prediction analysis was performed aligning RNA-Seq reads with BWA v. 0.6.1 [] with option bwasw and -T = 15. Gencode v19 was used as reference transcriptome dataset while hg19 a […]


The Circular RNA Profiles of Colorectal Tumor Metastatic Cells

Front Genet
PMCID: 5811837
PMID: 29479369
DOI: 10.3389/fgene.2018.00034
call_split See protocol

[…] For each circRNA-seq sample, FASTQ reads were first mapped to human genome (GRCh38/hg38) by BWA (Li and Durbin, ) and then CIRI2 (Gao et al., ) was used to identify circRNAs. The number of reads spanning back-spliced junctions was used as an absolute measure of circRNA abundance. While running CIRI2, default parameters we […]


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CIRI institution(s)
Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
CIRI funding source(s)
The National Natural Science Foundation of China (grant numbers 91640117 and 91531306), the National Key R&D Program (grant number 2016YFC1200804) and the Strategic Priority Research Program of the Chinese Academy of Sciences (grant number XDB13000000).

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