Cirit is a completely reference-free algorithm for genome-wide circular RNA (circRNA) detection from RNA sequencing (RNA-seq) transcriptome. This new algorithm, other than current BSJ-based algorithms, will provide direct sequence evidence for RNA circularization. It breaks the dependency of good quality genome in circRNA detection, and thus allows easy deployment to any organism, even under the circumstance of draft genome or no genome.

 de novo circRNA detection with full-length sequence: Cirit.jar
 Recovery of partially assembled circRNA: Patch (Applicable with reference genome)
 de novo circRNA detection with full-length sequence:

Prerequisites:
1. Undertake the RNA-seq dataset assembly in advance using de novo assembler such as IDBA-Trans or Velvet. The output transcriptome should be deposit as a single sequence file in *.fasta format. Please follow the best procedure of the assembler to obtain good transcriptome, which will substantially affect the circRNA detection.
2. Make sure the Java Runtime Environment (JRE) has been properly installed and is running. JRE version > 1.7 is recommended.

Options
usage: java -jar Cirit.jar -i <fasta> [OPTIONS]
-h,--help Print help
-i,--input <file>Input FASTA file
-o,--output <file>name of output file.
By default, the output file is put in current
directory, named "CircRNAs_Cirit.fa"
-w,--window <number>window/seed (integer), used to initial search.
By default, window is 10.

Quick Start
Put Cirit.jar and sequence file (e.g. seq.fasta) in the same working directory

For Linux/Unix user:
       $java -jar Cirit.jar –i seq.fasta

For Windows user:
       ## start the command prompt (cmd) and go to the working directory
       $java -jar Cirit.jar –i seq.fasta

 Recovery of partially assembled circRNA

Output:   CircRNAs_Cirit.fa

Recovery of partially assembled circRNA：

Step1: python Pred1 -genePredExt -geneNameAsName2 -r -o output.gene.Pred

Step2: python Pred2.py -o output.gene.Pred -i > circRNA_anno.bed

Step3: python Pred3.py circRNA_anno.bed -reference > circRNA_full.fasta

-r,--input hg19.gtf or hg38.gtf

-i,--input circRNA.bed

-reference,--input GRCh38.p10.genome.fa or GRCh19.p10.genome.fa
HepG2 circRNAs detected by Cirit are available for downloading
1.   CircRNA-enriched library (RNase R+/ribo-)

2.   Total RNA library (ribo-)
The Bioinformatics-Aided Drug Discovery Group (BADD)@Xiamen University declare the full copyright of this software. It is free for academic use.