miRSeq – A User-Friendly Standalone Toolkit for Sequencing Quality Evaluation and miRNA Profiling

MicroRNAs (miRNAs) present diverse regulatory functions in a wide range of biological activities. Studies on miRNA functions generally depend on determining miRNA expression profiles between libraries by using a next-generation sequencing (NGS) platform. Currently, several online web services are developed to provide small RNA NGS data analysis. However, the submission of large amounts of NGS data, conversion of data format, and limited availability of species bring problems.

In this study, researchers at the National Chiao Tung University, Taiwan developed miRSeq to provide alternatives. To test the performance, they had small RNA NGS data from four species, including human, rat, fly, and nematode, analyzed with miRSeq. The alignments results indicate that miRSeq can precisely evaluate the sequencing quality of samples regarding percentage of self-ligation read, read length distribution, and read category. miRSeq is a user-friendly standalone toolkit featuring a graphical user interface (GUI). After a simple installation, users can easily operate miRSeq on a PC or laptop by using a mouse. Within minutes, miRSeq yields useful miRNA data, including miRNA expression profiles, 3′ end modification patterns, and isomiR forms. Moreover, miRSeq supports the analysis of up to 105 animal species, providing higher flexibility.

rna-seqAvailability – The user can download miRSeq package via https://docs.google.com/forms/d/1WMsHS8jlxL-k3cL_UHTEKQGssno4ru6CuJMsGbPOqtk/viewform. Then, the user should first install the Perl complier and related modules by following the instructions in the readMe file. miRSeq is composed of two modules, including readPro and readMap, both of which can operate independently.

Pan CT et al. (2014) miRSeq: A User-Friendly Standalone Toolkit for Sequencing Quality Evaluation and miRNA Profiling. BioMed Research International [Epub ahead of print]. [article]