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Bioinformatics. 2018 Nov 21. doi: 10.1093/bioinformatics/bty948. [Epub ahead of print]

circtools - a one-stop software solution for circular RNA research.

Author information

1
Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.
2
DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany.

Abstract

Motivation:

Circular RNAs (circRNAs) originate through back-splicing events from linear primary transcripts, are resistant to exonucleases, are not polyadenylated, and have been shown to be highly specific for cell type and developmental stage. CircRNA detection starts from high-throughput sequencing data and is a multi-stage bioinformatics process yielding sets of potential circRNA candidates that require further analyses. While a number of tools for the prediction process already exist, publicly available analysis tools for further characterization are rare. Our work provides researchers with a harmonized workflow that covers different stages of in silico circRNA analyses, from prediction to first functional insights.

Results:

Here, we present circtools, a modular, Python-based framework for computational circRNA analyses. The software includes modules for circRNA detection, internal sequence reconstruction, quality checking, statistical testing, RNA binding protein enrichment screenings, differential exon RNase R resistance, and circRNA-specific primer design. Circtools supports researchers with visualization options and data export into commonly used formats.

Availability:

Circtools is available via github.com/dieterich-lab/circtools and circ.tools under GPLv3.0.

Supplementary information:

Supplementary data are available at Bioinformatics online.

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