Hisat2 Build L

hisat2-build-l

Quick Start

• Command: hisat2-build-l <reference_in> <ht2_index_base>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/hisat2-build-l
• Full reference: references/help.md

When To Use This Tool

• Use hisat2-build-l when the reference or graph augmentation is large enough that you need HISAT2 large-index output (.ht2l).
• It is appropriate when building splice-aware or graph-aware indexes that include SNPs, haplotypes, splice sites, exons, or repeat annotations.
• Use it when you deliberately want the large-index builder instead of letting hisat2-build auto-select the backend.
• This is the right preparatory step before hisat2-align-l.

Common Patterns

# Build a large HISAT2 index from one FASTA
hisat2-build-l genome.fa genome_large

# Build with splice sites and exons for RNA-seq alignment
hisat2-build-l genome.fa genome_large --ss splicesites.txt --exon exons.txt

# Include SNP and haplotype annotations
hisat2-build-l genome.fa genome_large --snp snps.txt --haplotype haplotypes.txt

# Use 8 threads during index construction
hisat2-build-l -p 8 genome.fa genome_large

Recommended Workflow

1. Prepare reference FASTA file(s) and optional annotation files (SNP, haplotype, splice sites, exons)
2. Run hisat2-build-l with reference input and desired index base name
3. Use -p flag to specify thread count for parallel processing
4. Verify generated .ht2l index files are present before running HISAT2 alignment

Guardrails

• The tool warns that hisat2-build wrapper is recommended over direct hisat2-build-l usage
• Use --bmax, --bmaxdivn, and --dcv options to manage memory for large references
• Output index files use .ht2l extension (large index format), not standard .ht2
• Pass only the basename to downstream aligners; do not append .ht2l suffixes manually