ASGAL requires the variables $fastqpair1suffix and $fastqpair2suffix to be set in the scripts/ file.


These are the default parameters set in the src/asgal/ script. If you want to change it you can do this in the ENTRYPOINT script directly. Please refer to the ASGAL manual.


Set multi option.


Reference genome in fasta format.

-g $fasta

The path to the gene annotation file in GTF format for annotation of fusion junctions.

-a $gtf

Transcript file.

-t $transcript

Fastq filename of paired end read 1.

-s *yourFastqFile1_*1.fastq

Fastq filename of paired end read 2.

-s2 *yourFastqFile1_*2.fastq

Output directory. The output will be separated into case and control folder based on the basefolder of the according fastq file.

-o $outdir

Number of threads to be used during the computation

-@ $ncores

Report all events, not only novel ones.