hisat2-build-s

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

hisat2-build-s

Quick Start

• Command: hisat2-build-s <reference_in> <ht2_index_base>
• 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

Recommended Workflow

1. Prepare reference sequence file(s) and optional annotation files (SNPs, haplotypes, splice sites, exons).
2. Run hisat2-build-s with reference input and desired index base name, using -p for multithreading.
3. Verify generated .ht2 index files are created at the specified base path.
4. Note the tool warning: consider using hisat2-build wrapper instead of hisat2-build-s directly.

Guardrails

• The tool recommends using hisat2-build wrapper instead of hisat2-build-s directly.
• Both <reference_in> and <ht2_index_base> arguments are required.
• Use -p <int> to control thread count based on available system resources.
• Downstream aligners should receive the basename only, without .ht2 suffixes