hisat2-inspect-s

name	hisat2-inspect-s
description	Use when extracting metadata, reference names, SNPs, splice sites, or exon information from HISAT2 index files (.ht2).
disable-model-invocation	true
user-invocable	true

hisat2-inspect-s

Quick Start

• Command: hisat2-inspect-s [options] <ht2_base>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/hisat2-inspect-s
• Full reference: See references/help.md for complete options and details

When To Use This Tool

• Use hisat2-inspect-s when you know the target index is the standard HISAT2 small format (.ht2) and want to inspect that binary directly.
• It is useful for extracting sequence names, summaries, and embedded graph annotations from a small index without wrapper auto-selection.
• Use it when validating a small-index build or debugging annotation content in a standard HISAT2 index.
• For general use, hisat2-inspect remains the more flexible entry point.

Common Patterns

# Summarize a standard HISAT2 index
hisat2-inspect-s -s genome

# List reference names only
hisat2-inspect-s -n genome

# Extract splice sites or exons embedded in the index
hisat2-inspect-s --ss genome > splicesites.txt
hisat2-inspect-s --exon genome > exons.txt

# Reconstruct FASTA from the index
hisat2-inspect-s -e genome > genome.fa

Recommended Workflow

1. Identify the HISAT2 index base name (filename minus .1.ht2/.2.ht2 suffix)
2. Run hisat2-inspect-s -s <ht2_base> to get a summary of index contents
3. Use -n for names only, or --snp/--ss/--exon for specific annotations
4. Redirect output to a file if extracting full FASTA sequences

Guardrails

• Provide the index base name without the .1.ht2/.2.ht2 extension
• Use -e/--ht2-ref sparingly; reconstructing references is slow
• Ensure the index files exist in the working directory or provide full paths
• The direct executable prints a wrapper-warning message; that warning is expected when calling hisat2-inspect-s directly