CIRI pipeline

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



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  • person_outline Fangqing Zhao <>

Publications for CIRI

CIRI IN pipelines

PMCID: 5366334
PMID: 28396678
DOI: 10.3389/fpls.2017.00413

[…] kiwifruit actin (achn107181) as endogenous control genes., to compare the expression of circrnas across various kiwifruit tissues and taxa, we calculated the accounts of backspliced reads from the ciri results for each circrna that was normalized by using the total sequencing reads in a corresponding sample data set (defined as reads per million mapped reads, rpm) as an indicator […]

PMCID: 5561264
PMID: 28819222
DOI: 10.1038/s41598-017-08806-0

[…] from the sequencing raw data using trimmomatic (version 0.32) (parameters: illuminaclip: adaptor.fa:2:30:10 leading:3 trailing:3 slidingwindow:4:15 minlen:50). the software segemehl (v 0.1.7) and ciri (v 2.0.5) were used for potential back-splice sites extraction41, 42., total rna was isolated by trizol reagent (life technologies, carlsbad, ca) followed by dna residue depletion using dnase […]

PMCID: 4656206
PMID: 26349458
DOI: 10.1007/s13238-015-0202-0

[…] rna-seq become the most prevalent method for identification of circrnas. although a few bioinformatic algorithms such as mapsplice (wang et al., 2010), tophat-fusion (kim and salzberg, 2011), and ciri (gao et al., 2015) were developed for global discovery of circular rnas, the consistency of these computational tools remains relatively low. rnase r treatment largely removes the false positive […]

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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