Hello, 
I found this code in Biostar handbook (RNA-Seq by Example) in section about genome indexing.

    # The reference genome.
    IDX=refs/genome.fa
    
    # Build the genome index.
    hisat2-build $IDX $IDX
    
    # Index the reference genome with samtools.
    samtools faidx $IDX

I was wondering about samtools indexing step. I've never seen anyone using it before. Isn't hisat2-build not enough to properly index genome? 
Yes, the HISAT2 indexing step is enough :)