AlgoLab / galig

A graph aligner
GNU General Public License v3.0
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ASGAL

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 main idea behind ASGAL is the following one: the alternative splicing events can be detected by aligning the RNA-Seq reads against the splicing graph of the gene.

The instructions to install and use ASGAL are at http://asgal.algolab.eu.

Prerequisites

See here for more details.

Compiling

git clone --recursive https://github.com/AlgoLab/galig.git
cd galig
make prerequisites
make

Running

./asgal -g [genome] -a [annotation] -s [sample] -o outputFolder

In more detail:

# Align RNA-Seq reads to a splicing graph
./bin/SpliceAwareAligner -g [reference] -a [annotation] -s [sample] -o outputFolder/output.mem

# Convert alignments to SAM format
python3 ./scripts/formatSAM.py -m output.mem -g [reference] -a [anotation] -o outputFolder/output.sam

# Detect events from alignments
python3 ./scripts/detectEvents.py -g [reference] -a [annotation] -m output.mem -o outputFolder/output.events.csv

Example

cd example
tar xfz input.tar.gz
../asgal -g ./input/genome.fa -a ./input/annotation.gtf -s ./input/sample_1.fa -o outputFolder

This command will produce four files in the output folder:

An extended explanation of this example can be found here.

The tool has been tested only on 64bit Linux system. You can find more information at http://asgal.algolab.eu.

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