HopedWall / galig

A graph aligner

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

• python3
• biopython
• pysam
• gffutils
• cmake
• samtools
• zlib1g-dev
• boost

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/reads.fasta -o outputFolder

This command will produce four files in the output folder:

• a .mem file containing the alignments to the splicing graph
• a .sam file, containing the alignments to the splicing graph mapped to the reference genome
• a .events.csv file, containing the alternative splicing events detected in the RNA-Seq sample
• a .log file, containing the log of the execution

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.