SUMMARY: High-throughput sequencing currently generates a wealth of small RNA (sRNA) data, making data mining a topical issue. Processing of these large data-sets is inherently multidimensional as length, abundance, sequence composition, and genomic location all hold clues to sRNA function. Analysis can be challenging because the formulation and testing of complex hypotheses requires combined use of visualization, annotation, and abundance profiling. To allow flexible generation and querying of these disparate types of information, we have developed the shortran pipeline for analysis of plant or animal short RNA sequencing data. It comprises nine modules and produces both graphical and MySQL format output. AVAILABILITY: shortran is freely available and can be downloaded from http://users-mb.au.dk/pmgrp/shortran/Contacts: firstname.lastname@example.org, email@example.com SUPPLEMENTARY INFORMATION: Supplementary data is available at Bioinformatics online.