bowtie2-inspect-s

name	bowtie2-inspect-s
description	Use when you need to inspect Bowtie 2 index files to extract reference sequence names, lengths, or index summary information from .bt2 files.
disable-model-invocation	true
user-invocable	true

bowtie2-inspect-s

Quick Start

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

When To Use This Tool

• Use bowtie2-inspect-s when you know the index is the standard Bowtie 2 small format (.bt2) and want to inspect that binary directly.
• It is useful for recovering sequence names, printing summaries, or reconstructing FASTA from a small index.
• Use it when you want to avoid ambiguity between small and large index formats during debugging or validation.
• In general-purpose workflows, bowtie2-inspect is still the better default entry point.

Common Patterns

# Summarize a standard Bowtie 2 index
bowtie2-inspect-s -s ref

# List only reference names
bowtie2-inspect-s -n ref

# Reconstruct FASTA from the index
bowtie2-inspect-s ref > ref.fa

# Save summary output directly to a file
bowtie2-inspect-s -s ref -o ref.summary.txt

Recommended Workflow

1. Identify the Bowtie 2 index base name (path without .1.bt2/.2.bt2 suffix)
2. Run bowtie2-inspect-s -s <bt2_base> to print a summary including reference names, lengths, and index properties
3. Use -n to list only reference names, or omit flags for FASTA output
4. Save output to a file using -o <filename> or redirect stdout

Guardrails

• Requires valid Bowtie 2 index files (.bt2) present at the specified base path
• The <bt2_base> argument must exclude trailing .1.bt2/.2.bt2 extensions
• This is a direct executable; prefer the wrapper script if available
• The direct executable emits a wrapper warning message; that warning is normal when calling bowtie2-inspect-s directly