Requirement
fasta sequence of custom genome/genome scaffolds
Two-staged process
Run1:
The first time running sarek specify the custom fasta file (--fasta mygenome.fa) and add the option to save reference sequence (--save_reference)
Sarek will generate a bed, BWAIndex files etc it saved them to the results folder.
Copy generated files to reference folder and updated the qutgenomes.config file
Run 2:
sarek pipeline is run using generated files in run1