| 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
hisat2-build -p 8 reference.fa ref_index
hisat2-build \
-p 8 \
--ss splicesites.txt \
--exon exons.txt \
reference.fa \
ref_index
hisat2-build --large-index reference.fa ref_index
Recommended Workflow
- Start from the exact reference FASTA used across the RNA-seq project.
- Add splice-site and exon files if you want a more annotation-aware index.
- Keep the index basename stable for reproducible pipeline configuration.
- 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.
