# # Downloads a reference genome and indexes it with bwa. # # Initialize the "real" genome to match the reference. # # Stop on any error. set -uex # Reference genome accession number. ACC=AF086833 # Directory for the reference files. REF=refs # Make the reference directory. mkdir -p $REF # Reference genome file name. REFERENCE=$REF/${ACC}.fa # The "real" genome that will be modified. GENOME=genome.fa # Fetch the genome from the accession. efetch -db nucleotide -id $ACC -format fasta > $REFERENCE # Index the genome with bwa. You may comment this out on second runs. bwa index $REFERENCE # Initially the real genome is the same as the reference. cp $REFERENCE $GENOME