ASGAL (Alternative Splicing Graph ALigner) is a tool for detecting the alternative splicing events expressed in a RNA-Seq sample with respect to a gene annotation. The ASGAL approach consists of some steps:

  1. splicing graph construction: from the gene annotation, ASGAL builds the splicing graph representing the gene structure that is implied by the set of input transcripts.
  2. splice-aware alignment: ASGAL aligns the RNA-Seq reads against the splicing graph of the input gene. This procedure is tailored for such kind of alignments.
  3. detection of the alternative splicing events: the spliced alignments are analyzed to detect the alternative splicing events that are induced by the reads in the sample. Moreover ASGAL can report all events found, or only those that are not in the input annotation.

Alternative Splicing Events

Actually, ASGAL fully supports the following alternative splicing events:

  • exon skipping
  • alternative acceptor site
  • alternative donor site
  • intron retention (caused by the insertion of a new intron inside an exon)


If you use ASGAL, please cite its use as:

Luca Denti, Raffaella Rizzi, Stefano Beretta, Gianluca Della Vedova, Marco Previtali and Paola Bonizzoni. ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events (BMC Bioinformatics, bibtex)


ASGAL is available at Docker Hub. A detailed installation walkthrough and the documentation is available.


The example directory contains a small dataset on the gene CG13375 of Drosophila Melanogaster.

If you already have docker installed, you can run ASGAL on that sample with the commands

tar xfz input.tar.gz
docker run -v "$PWD"/input:/data algolab/asgal

The running times will be a few seconds. Then you will find the file in the input directory. An extended explanation of this example can be found here.


If you have any question or you have any problem using the tool, please contact Luca Denti. Alternatively, you can use the issue tracker.