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 <>

CIRI articles

CIRI citations

PMCID: 5814174

[…] 19 bp were reported. bwa-mem allows split alignment which is vital for circular rna detection. bwa-mem aligned reads were then processed by ciri (downloaded from for circrna detection and abundance calculation. ciri determines circrnas by the presence of paired chiastic clipping signals where two segments of a junction read was mapped to the reference […]

PMCID: 5366334

[…] 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 […]

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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