High-throughput RNA sequencing allows genome-wide analyses of pre-mRNA splicing across multiple conditions. However, the increasing number of available datasets represents a major challenge in terms of time and storage required for analyses. Here we describe SUPPA, a computational pipeline to calculate relative inclusion values of alternative splicing events, exploiting fast transcript quantification of a known annotation. SUPPA provides a fast and accurate approach to calculate inclusion levels of alternative splicing events from a large number of samples, thereby facilitating systematic analyses in the context of large-scale projects using limited computational resources. SUPPA is available at https://bitbucket.org/regulatorygenomicsupf/suppa under the MIT license and is implemented in Python 2.7.