Prepare fasta with .fai and .dict

If you want to use a public aviliable reference.fasta, eg. Drosophila Melanogaster r6.39 from FlyBase.

mkdir Ref_genome
cd Ref_genome
wget http://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6.39_FB2021_02/fasta/dmel-all-chromosome-r6.39.fasta.gz

# Unizip .gz
gunzip dmel-all-chromosome-r6.39.fasta.gz
# Create .fai
bwa index dmel-all-chromosome-r6.39.fasta

This step creates

.fasta.amb
.fasta.ann
.fasta.bwt
.fasta.pac
.fasta.sa