hisat2-build

name	hisat2-build
description	Use when building HISAT2 index files from reference genomes for subsequent alignment with hisat2. Handles FASTA reference inputs and creates .ht2 index files.
disable-model-invocation	true
user-invocable	true

hisat2-build

Quick Start

• Command: hisat2-build [options]* <reference_in> <ht2_index_base>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/hisat2-build
• Version: 2.2.2
• Full reference: See references/help.md for complete options and details

When To Use This Tool

• Build a standard or graph-aware HISAT2 index from reference FASTA.
• Add splice sites, exons, SNPs, or haplotypes into the index when the workflow benefits from them.
• Rebuild the index when the reference or annotations change.
• Use before hisat2 whenever the .ht2 files do not already exist.

Common Patterns

# 1) Basic HISAT2 index build
hisat2-build -p 8 reference.fa ref_index

# 2) Build with splice sites and exons
hisat2-build \
  -p 8 \
  --ss splicesites.txt \
  --exon exons.txt \
  reference.fa \
  ref_index

# 3) Force a large index
hisat2-build --large-index reference.fa ref_index

Recommended Workflow

1. Start from the exact reference FASTA used across the RNA-seq project.
2. Add splice-site and exon files if you want a more annotation-aware index.
3. Keep the index basename stable for reproducible pipeline configuration.
4. Confirm all expected .ht2 files exist before aligning.

Guardrails

• Annotation sidecar files (--ss, --exon, --snp, --haplotype) must match the same reference build used in FASTA.
• --large-index is needed for very large references and changes the resulting index format.
• -c means sequence text is supplied on the command line, which is rarely appropriate for real genomes.
• Building graph-aware indexes adds complexity; use only the annotation inputs you actually trust.