SGAL (Splicing Graph ALigner)

Splicing Graph ALigner (SGAL) is a tool for mapping one or more RNA-Seq samples against the splicing graph of a gene with the main goals of computing the spliced alignments of the input samples and identifying the alternative splicing events expressed in the samples with respect to the gene annotation.



The tools takes in input: a reference genome (FASTA format), a gene annotation (GTF format) and a set of RNA-Seq samples (FASTA or FASTQ format) and produces in output the spliced alignments (SAM format) and the list of alternative splicing events identified in the samples (CSV format). Moreover, if more samples are given in input, the tool outputs also a summary table (CSV format) that compares the events identified in the different input samples.


The Approach

SGAL works as follows:

  1. it builds the splicing graph using the reference genome and the gene annotation
  2. it computes the matches between the splicing graph and each RNA-Seq sample
  3. it converts the matches in spliced alignments (to the reference genome)
  4. it detects the alternative splicing events expressed in the samples using the matches computed in the previous step


Beretta, S., Bonizzoni, P., Denti, L., Previtali, M., Rizzi, R. (2017). Mapping RNA-seq Data to a Transcript Graph via Approximate Pattern Matching to a Hypertext. AlCoB: 49-61.

Downloads and support

The software is freely available at