tinyRNA: precision analysis of small RNA-seq data with user-defined hierarchical selection rules

Abstract

SummarytinyRNA performs precision analysis of small RNAs, including miRNAs, piRNAs, and siRNAs, from high-throughput sequencing experiments. At the core of tinyRNA is a highly flexible counting utility, tiny-count, that allows for hierarchical assignment of small RNA reads to features based on positional information, extent of feature overlap, 5 nucleotide, length, and strandedness. tinyRNA provides an all-in-one solution for small RNA-seq data analysis, with documentation and statistics generated at each step for accurate, reproducible results. Availability and ImplementationtinyRNA tools are implemented in Python and R, and the pipeline workflow is coordinated with CWL. tinyRNA is free and open-source software distributed under the GPLv3 license. tinyRNA is available at https://github.com/MontgomeryLab/tinyRNA. Contacttai.montgomery@colostate.edu Supplementary informationReference data, including genome sequences and features tables, for certain species can be found at https://www.MontgomeryLab.org.