Imported from vimalinx/bio-agent (.claude/skills/bowtie2-inspect/SKILL.md). Install upstream with npx skills add vimalinx/bio-agent --skill bowtie2-inspect. Copyright stays with the author.

bowtie2-inspect

Quick Start

• Command: bowtie2-inspect [options] <bt2_base>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/bowtie2-inspect
• Full reference: See references/help.md

When To Use This Tool

• Use bowtie2-inspect when you need to recover sequences, names, or metadata from an existing Bowtie 2 index basename.
• It is the generic inspector and is the right first choice when you are not manually forcing the small or large direct executable.
• Use -n for name-only output, -s for a summary, and the default mode when you want FASTA reconstructed from the index.
• Use --large-index if both small and large forms are present and you need to force inspection of the large index.

Common Patterns

# Print a summary of the index
bowtie2-inspect -s ref

# List reference names only
bowtie2-inspect -n ref

# Recover FASTA from the index
bowtie2-inspect ref > ref_from_index.fa

# Force inspection of a large index
bowtie2-inspect --large-index -s ref_large

Recommended Workflow

1. Verify the index base name (without .1.bt2/.2.bt2 suffix)
2. Run bowtie2-inspect -s <bt2_base> to get a summary of the index
3. Use -n to list reference names only, or run without flags for FASTA output
4. Save output with -o <filename> or redirect to a file

Guardrails

• Provide the bt2 base name without trailing .1.bt2/.2.bt2 extensions
• Output goes to stdout by default; use -o or shell redirection to save
• Use --large-index only when forcing inspection of a large-format index