SUPPA – a super-fast pipeline for alternative splicing analysis from RNA-Seq

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.

Now, a team led by researchers at the Universitat Pompeu Fabra have developed 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.


Availability – SUPPA is available at under the MIT license and is implemented in Python 2.7.

Alamancos GP, Pagès A, Trincado JL, Bellora N, Eyras E. (2014) SUPPA: a super-fast pipeline for alternative splicing analysis from RNA-Seq. bioRxiv [Epub ahead of print]. [abstract]