bowtie2-inspect
Inspects Bowtie2 indexes to retrieve reference sequences and index metadata.
Install
mkdir -p .claude/skills/bowtie2-inspect && curl -L -o skill.zip "https://agentskills.codes/api/skills/download/18176" && unzip -o skill.zip -d .claude/skills/bowtie2-inspect && rm skill.zipInstalls to .claude/skills/bowtie2-inspect
Activation
This is the description your AI agent reads to decide when to run this skill — the better it matches your request, the more reliably it fires.
Use when you need to extract reference sequences, names, or summary information from a Bowtie2 index file.Key capabilities
- →Extract reference sequences from a Bowtie2 index
- →List reference names from an index
- →Obtain a summary of an index
- →Reconstruct FASTA sequences from an index base
- →Force inspection of a large-format index
- →Save output to a file
How it works
The tool `bowtie2-inspect` extracts information from an existing Bowtie2 index file, allowing users to retrieve reference sequences, names, or a summary.
Inputs & outputs
When to use bowtie2-inspect
- →Inspecting bioinformatics indexes
- →Retrieving reference sequence names
- →Summarizing index metadata
About this skill
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-inspectwhen 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
-nfor name-only output,-sfor a summary, and the default mode when you want FASTA reconstructed from the index. - Use
--large-indexif 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
- Verify the index base name (without
.1.bt2/.2.bt2suffix) - Run
bowtie2-inspect -s <bt2_base>to get a summary of the index - Use
-nto list reference names only, or run without flags for FASTA output - Save output with
-o <filename>or redirect to a file
Guardrails
- Provide the bt2 base name without trailing
.1.bt2/.2.bt2extensions - Output goes to stdout by default; use
-oor shell redirection to save - Use
--large-indexonly when forcing inspection of a large-format index
When not to use it
- →When the user needs to build a Bowtie2 index
- →When the user needs to align reads to a reference
- →When the user is manually forcing the small or large direct executable
Limitations
- →Requires the Bowtie2 index base name without extensions
- →Output goes to stdout by default
- →The tool is for inspection, not for creating or modifying indexes
How it compares
This tool provides direct command-line access to inspect and extract data from a Bowtie2 index, offering specific flags for names, summaries, or FASTA reconstruction, unlike general file inspection utilities.
Compared to similar skills
bowtie2-inspect side by side with the closest alternatives in the catalog.
| Skill | Installs | Updated | Safety | Difficulty |
|---|---|---|---|---|
| bowtie2-inspect (this skill) | 0 | 3mo | Review | Beginner |
| streamlit | 86 | 9mo | No flags | Intermediate |
| jupyter-notebook | 30 | 5mo | Review | Intermediate |
| backtesting-frameworks | 17 | 2mo | No flags | Advanced |
Try saying
Example prompts that trigger this skill in your AI assistant.
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