Genome indexing with hisat2 and samtools
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?
2 answers
Yes, the HISAT2 indexing step is enough :)
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Rafael Soler •
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