Genome indexing with hisat2 and samtools

Question

[MK]

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?

Answer 1

[Rafael Soler]

Yes, the HISAT2 indexing step is enough :)

Answer 2

[GenoMax]

samtools index fasta is required for querying fasta files, extracting regions from fasta file.