I am trying to index a reference genome using bwa index.
bwa index -a bwtsw xxx.fasta
It runs without errors and generates the following files with extensions .amb,.ann,.bwt,.pac,.sa.
I have never really done indexing myself before using bwa.However, I remember indexing generates other files as well such as .rpac,.rbwt,.rpac,.rsa.What does r indicate here? What are the files generated usually when we index a reference genome ? Any help is appreciated.