Journal Article

unitas: the universal tool for annotation of small RNAs

Gebert, Daniel, Hewel, Charlotte, Rosenkranz, David

2017

Overview

Background Next generation sequencing is a key technique in small RNA biology research that has led to the discovery of functionally different classes of small non-coding RNAs in the past years. However, reliable annotation of the extensive amounts of small non-coding RNA data produced by high-throughput sequencing is time-consuming and requires robust bioinformatics expertise. Moreover, existing tools have a number of shortcomings including a lack of sensitivity under certain conditions, limited number of supported species or detectable sub-classes of small RNAs. Results Here we introduce unitas, an out-of-the-box ready software for complete annotation of small RNA sequence datasets, supporting the wide range of species for which non-coding RNA reference sequences are available in the Ensembl databases (currently more than 800). unitas combines high quality annotation and numerous analysis features in a user-friendly manner. A complete annotation can be started with one simple shell command, making unitas particularly useful for researchers not having access to a bioinformatics facility. Noteworthy, the algorithms implemented in unitas are on par or even outperform comparable existing tools for small RNA annotation that map to publicly available ncRNA databases. Conclusions unitas brings together annotation and analysis features that hitherto required the installation of numerous different bioinformatics tools which can pose a challenge for the non-expert user. With this, unitas overcomes the problem of read normalization. Moreover, the high quality of sequence annotation and analysis, paired with the ease of use, make unitas a valuable tool for researchers in all fields connected to small RNA biology.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V
• Subject: Algorithms / Animal Genetics and Genomics / Annotations / Applications software / Bioinformatics / Biology / Biomedical and Life Sciences / Datasets / Gene sequencing / Genomics / HeLa Cells / High-Throughput Nucleotide Sequencing / Humans / Library collections / Life Sciences / Linux / Microarrays / Microbial Genetics and Genomics / MicroRNA / Molecular Sequence Annotation - methods / Next-generation sequencing / Non-coding RNA / Nucleotide sequence / Online data bases / Plant Genetics and Genomics / Proteomics / RNA, Small Untranslated - genetics / Software / Transcriptomic methods / URLs