sRNAfrag: A pipeline and suite of tools to analyze fragmentation in small RNA sequencing data

Abstract

Fragments derived from RNAs such as small nucleolar RNAs hold biological relevance. However, they remain poorly understood which calls for more comprehensive methods to analyze such fragmentation. Thus, we developed sRNAfrag, a standardized workflow and set of scripts for quantifying and analyzing sRNA fragmentation. It is able to detect start and end loci of mature microRNAs fragmented from precursors and, utilizing multi-mapping events, the conserved 5' seed sequence of miRNAs. The tool detected 1411 snoRNA fragment conservation events between 2/4 eukaryotic species, providing the opportunity to explore motifs and fragmentation patterns not only within species, but between. Availability: https://github.com/kenminsoo/sRNAfrag.