Genome indexing with hisat2 and samtools
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11 months ago
MK ▴ 30

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 • 540 views
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Entering edit mode
11 months ago
Rafael Soler ▴ 460

Yes, the HISAT2 indexing step is enough :)

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11 months ago
GenoMax 118k

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

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