hisat2-inspect-l

name	hisat2-inspect-l
description	Use when you need to inspect or extract information from HISAT2 large index files (.ht2l), including reference sequences, splice sites, SNPs, exons, or index summaries.
disable-model-invocation	true
user-invocable	true

hisat2-inspect-l

Quick Start

• Command: hisat2-inspect-l [options] <ht2_base>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/hisat2-inspect-l
• Full reference: references/help.md

When To Use This Tool

• Use hisat2-inspect-l when you know the target index is the large HISAT2 format (.ht2l) and want to inspect it directly.
• It is useful for debugging large-index builds, checking embedded SNP/splice/exon annotations, or reconstructing reference content.
• Use it when you want to avoid ambiguity about whether the wrapper will resolve to the small or large index flavor.
• In routine cases, the generic hisat2-inspect wrapper is still the better default.

Common Patterns

# Summarize a large HISAT2 index
hisat2-inspect-l -s genome_large

# List reference names only
hisat2-inspect-l -n genome_large

# Extract embedded SNPs or splice sites
hisat2-inspect-l --snp genome_large > snps.txt
hisat2-inspect-l --ss genome_large > splicesites.txt

# Reconstruct the reference from a large index
hisat2-inspect-l -e genome_large > genome_large.fa

Recommended Workflow

1. Run with -s/--summary first to understand index contents and properties
2. Use -n/--names to list reference sequence names without full output
3. Extract specific features as needed (--snp, --ss, --exon)
4. Use -e/--ht2-ref only when you need to reconstruct the full reference (slow)

Guardrails

• The <ht2_base> argument is the ht2 filename minus trailing .1.ht2l/.2.ht2l
• Reconstructing reference with -e/--ht2-ref is slow; prefer -s or -n for quick inspection
• Output defaults to FASTA format to stdout; redirect or pipe as needed
• The direct executable prints a wrapper-warning message; that warning is expected when calling hisat2-inspect-l directly