hisat2-inspect

name	hisat2-inspect
description	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.
disable-model-invocation	true
user-invocable	true

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 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

# 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