# Hisat2 Inspect

> Use when you need to inspect HISAT2 index files, extract reference sequences, view index summaries, or retrieve SNP/splice site/exon information from a .ht2 index.

- Skill: `vimalinx/hisat2-inspect` (Agent Skill, multi-file: 2 files)
- Install (CLI): `npx skillmds add vimalinx/hisat2-inspect`
- Raw SKILL.md: https://api.skillmd.com/api/skills/vimalinx/hisat2-inspect/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: vimalinx (https://skillmd.com/u/vimalinx)
- Updated: 2026-09-09
- Page: https://skillmd.com/skills/vimalinx/hisat2-inspect

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# hisat2-inspect

## Quick Start

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

## When To Use This Tool

- Use `hisat2-inspect` when you need to audit what is stored inside a HISAT2 index basename before alignment or debugging.
- It is the generic entry point for recovering FASTA, listing reference names, printing summaries, or extracting embedded SNP/splice/exon annotations.
- Use `--large-index` when you need to force inspection of a large index even if a small one is also present.
- Reach for this wrapper before the `-s` and `-l` direct executables unless you specifically need to pin the index flavor.

## Common Patterns

```bash
# Summarize a HISAT2 index
hisat2-inspect -s genome

# List reference names only
hisat2-inspect -n genome

# Extract embedded splice sites and exons
hisat2-inspect --ss genome > splicesites.txt
hisat2-inspect --exon genome > exons.txt

# Reconstruct FASTA from the index
hisat2-inspect genome > genome_from_index.fa
```

## Recommended Workflow

1. Identify the `.ht2` index base name (filename minus trailing `.1.ht2`/`.2.ht2`)
2. Run `hisat2-inspect -s <ht2_base>` to view a summary of index contents and parameters
3. Use `-n` to list reference names only, or run without flags to output full FASTA sequences
4. Add `--snp`, `--ss`, or `--exon` flags as needed to extract specialized annotation data

## Guardrails

- Provide the index base name without the `.1.ht2`/`.2.ht2` suffix, not the full filename
- Extracting full FASTA with `-e/--ht2-ref` is slow; prefer default output unless color preservation is required
- Use `--large-index` flag only when forcing inspection of a large index variant