Hello Riccardo,
This is a excellent work. I want to use your pipeline. However, I am confused for the “old” genome. This is mean reference genome?
Thanks,
Fuyou

The above call is composed of:

bash -> to specify that we are about to call a bash script
main.sh -> the main script of GenomeDelta.
--fq -> the FASTQ file of the “old” genome.
--fa -> the FASTA file of the “new” genome (the assembly).
--of -> the output folder.
--prefix -> the prefix that all the output files will have.
--t -> the number of threads that will be used to parallelize the slowest steps.
Remember to index the FASTA assembly before the call!