Use when building a HISAT2 graph-based index from reference sequences for splice-aware RNA-seq alignment, optionally incorporating SNPs, haplotypes, splice sites, or exon annotations.
name: hisat2-build-s
description: Use when building a HISAT2 graph-based index from reference sequences for splice-aware RNA-seq alignment, optionally incorporating SNPs, haplotypes, splice sites, or exon annotations.
disable-model-invocation: true
user-invocable: true
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/hisat2-build-s
Full reference: See references/help.md for complete options and usage details.
When To Use This Tool
Use hisat2-build-s when building a standard HISAT2 small index (.ht2) for typical genome sizes.
It is suitable for graph-aware index generation that augments the reference with SNPs, haplotypes, splice sites, exons, or repeat annotations.
Use it when you specifically want to force the small-index builder rather than rely on hisat2-build wrapper logic.
This is the normal upstream step before hisat2-align-s.
Common Patterns
# Build a standard HISAT2 index from one FASTA
hisat2-build-s genome.fa genome
# Add splice sites and exon annotations for RNA-seq alignment
hisat2-build-s genome.fa genome --ss splicesites.txt --exon exons.txt
# Include SNP and haplotype annotations
hisat2-build-s genome.fa genome --snp snps.txt --haplotype haplotypes.txt
# Parallelize index construction
hisat2-build-s -p 8 genome.fa genome