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Circular RNA detection software tools | RNA sequencing data analysis

Recent studies reveal that circular RNAs (circRNAs) are a novel class of abundant, stable and ubiquitous noncoding RNA molecules in animals. Comprehensive detection of circRNAs from high-throughput transcriptome data is an initial and crucial step…
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find_circ
Desktop

find_circ

Detects head-to-tail spliced (back-spliced) sequencing reads, indicative of…

Detects head-to-tail spliced (back-spliced) sequencing reads, indicative of circular RNA (circRNA) in RNA-seq data. find_circ is used extensively by circBase.

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Segemehl
Desktop

Segemehl

Maps short sequencer reads to reference genomes. Segemehl is a read aligner…

Maps short sequencer reads to reference genomes. Segemehl is a read aligner that allows to detect mismatches, insertions and deletions. The software implements a matching strategy based on enhanced…

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MapSplice
Desktop

MapSplice

A splice detection algorithm whose focus is high sensitivity and specificity in…

A splice detection algorithm whose focus is high sensitivity and specificity in the detection of splices as well as CPU and memory efficiency. MapSplice performs a sensitive, complete and unbiased…

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CIRCexplorer
Desktop

CIRCexplorer

A combined strategy to identify junction reads from back spliced exons and…

A combined strategy to identify junction reads from back spliced exons and intron lariats. CIRCexplorer is now only a circular RNA annotating tool, and it parses fusion junction information from…

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SUPeR-seq
Desktop

SUPeR-seq

A single-cell RNAseq technique which can detect both polyA+ mRNAs and polyA–…

A single-cell RNAseq technique which can detect both polyA+ mRNAs and polyA– RNAs from a single mammalian cell. SUPeR-seq has been successfully applied for investigating polyA– RNAs including…

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PcircRNA_finder
Desktop

PcircRNA_finder

Allows exonic circRNA prediction in plants. PcircRNA_finder is composed of…

Allows exonic circRNA prediction in plants. PcircRNA_finder is composed of several modules including: (1) Catcher that collects all backsplice sites by chiastic clipping mapping of PE reads; (2)…

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DCC
Desktop

DCC

Detects circRNAs from chimeric reads. DCC uses output from the STAR read mapper…

Detects circRNAs from chimeric reads. DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies a series of filters and…

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CIRI
Desktop

CIRI

Identifies circular RNAs (circRNAs) using multiple seed matching. CIRI is…

Identifies circular RNAs (circRNAs) using multiple seed matching. CIRI is designed to differentiate back-spliced junction (BSJ) reads from non-BSJ reads using efficient maximum likelihood estimation…

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UROBORUS
Desktop

UROBORUS

A computational pipeline to detect circular RNA from RNA-Seq data, based on…

A computational pipeline to detect circular RNA from RNA-Seq data, based on junction reads from back spliced exons. By applying UROBORUS to RNA-seq data from 46 gliomas and normal brain samples, we…

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NCLscan
Desktop

NCLscan

A high accurate method for detecting intragenic and intergenic non-co-linear…

A high accurate method for detecting intragenic and intergenic non-co-linear (NCL) transcripts. NCLscan utilizes a stepwise alignment strategy to almost completely eliminate false calls (>98%…

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CircPro
Desktop

CircPro

Identifies Circular RNAs (circRNAs) with protein-coding potential. CircPro can…

Identifies Circular RNAs (circRNAs) with protein-coding potential. CircPro can detect circRNAs, predict their protein-coding potential and discovering junction reads from Ribo-Seq data. It provides…

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Sailfish-cir
Desktop

Sailfish-cir

Estimates the relative abundance of circular RNA transcripts from…

Estimates the relative abundance of circular RNA transcripts from high-throughput RNA-seq data. Sailfish-cir transforms circular transcripts to pseudo-linear transcripts. Comparing to count-based…

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hppRNA
Desktop

hppRNA

Converts the raw fastq files into gene/isoform expression matrix and…

Converts the raw fastq files into gene/isoform expression matrix and differentially expressed genes or isoforms. hppRNA is a one-in-all solution composed of four scenarios such as pre-mapping,…

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KNIFE
Desktop

KNIFE

Increases the sensitivity and specificity of circular RNA detection by…

Increases the sensitivity and specificity of circular RNA detection by discovering and quantifying circular and linear RNA splicing events at both annotated and un-annotated exon boundaries,…

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CircTest
Desktop

CircTest

Tests the variation of circRNAs in respect to host genes. Ratio of circular…

Tests the variation of circRNAs in respect to host genes. Ratio of circular junction read counts to average total counts at exon borders can be shown along with the p-values.

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CirComPara
Desktop

CirComPara

Allows to detect, quantify and annotate circRNAs from RNA-seq data. CirComPara…

Allows to detect, quantify and annotate circRNAs from RNA-seq data. CirComPara permits to annotate circRNAs in terms of overlapping genes, in order to quantify linear RNAs and gene expression. It…

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Circmarker
Desktop

Circmarker

Detects circular RNA. Circmarker is based on k-mers rather than reads mapping.…

Detects circular RNA. Circmarker is based on k-mers rather than reads mapping. It creates k-mer table for circular RNA detection by using transcriptome annotation files. The tool was compared to…

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PTESFinder
Desktop

PTESFinder

Identifies putative post-transcriptional exon shuffling (PTES) structures by…

Identifies putative post-transcriptional exon shuffling (PTES) structures by mapping RNAseq reads to sequence models generated using existing transcript annotation. PTESFinder applies a series of…

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FUCHS
Desktop

FUCHS FUll CHaracterization of circular RNA using RNA Sequencing

Characterizes circRNAs candidates. FUCHS provides the user with directions for…

Characterizes circRNAs candidates. FUCHS provides the user with directions for further steps to investigate the circRNA’s function and biogenesis. FUCHS is able to identify alternative exon usage…

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circRNA_finder
Desktop

circRNA_finder

A software pipeline for finding circular RNAs from RNA-seq data, based on STAR.…

A software pipeline for finding circular RNAs from RNA-seq data, based on STAR. circRNA_finder has the capacity to identify circRNAs with very proximal splice sites (below 100 bp).

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Acfs
Desktop

Acfs Accurate circRNA finder suite

Allows circRNA identification and quantification. Acfs can handle both…

Allows circRNA identification and quantification. Acfs can handle both single-end (SE) and paired-end (PE) data. It consists of three main steps: (1) preprocessing - reads are collapsed, indexed and…

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circRNAFinder
Desktop

circRNAFinder

A software tool for identifying circRNAs using RNA deep sequencing data, as…

A software tool for identifying circRNAs using RNA deep sequencing data, as well as annotating and visualizing circRNAs and comparing their expression in different tissues or growth conditions.

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