Genome indexing with hisat2 and samtools

Genome indexing with hisat2 and samtools

0

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?


samtools


index


Hisat2


RNA-seq


genome

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2 hours ago by


MK

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