kraken2-taxonomic-classifier

Kraken2 taxonomic classification skill for rapid metagenomic read assignment

509 stars

Best use case

kraken2-taxonomic-classifier is best used when you need a repeatable AI agent workflow instead of a one-off prompt.

Kraken2 taxonomic classification skill for rapid metagenomic read assignment

Teams using kraken2-taxonomic-classifier should expect a more consistent output, faster repeated execution, less prompt rewriting.

When to use this skill

You want a reusable workflow that can be run more than once with consistent structure.

When not to use this skill

You only need a quick one-off answer and do not need a reusable workflow.
You cannot install or maintain the underlying files, dependencies, or repository context.

Installation

Claude Code / Cursor / Codex

$curl -o ~/.claude/skills/kraken2-taxonomic-classifier/SKILL.md --create-dirs "https://raw.githubusercontent.com/a5c-ai/babysitter/main/library/specializations/domains/science/bioinformatics/skills/kraken2-taxonomic-classifier/SKILL.md"

Manual Installation

Download SKILL.md from GitHub
Place it in .claude/skills/kraken2-taxonomic-classifier/SKILL.md inside your project
Restart your AI agent — it will auto-discover the skill

How kraken2-taxonomic-classifier Compares

Feature / Agent	kraken2-taxonomic-classifier	Standard Approach
Platform Support	Not specified	Limited / Varies
Context Awareness	High	Baseline
Installation Complexity	Unknown	N/A

Frequently Asked Questions

What does this skill do?

Kraken2 taxonomic classification skill for rapid metagenomic read assignment

Where can I find the source code?

You can find the source code on GitHub using the link provided at the top of the page.

SKILL.md Source

# Kraken2 Taxonomic Classifier Skill

## Purpose
Provide Kraken2 taxonomic classification for rapid metagenomic read assignment.

## Capabilities
- k-mer based classification
- Custom database creation
- Confidence score filtering
- Bracken abundance estimation
- Multi-sample reporting
- Memory-efficient operation

## Usage Guidelines
- Build or download appropriate databases
- Set confidence thresholds for accuracy
- Use Bracken for abundance estimation
- Generate reports for visualization
- Consider memory requirements
- Document database versions

## Dependencies
- Kraken2
- Bracken
- Centrifuge

## Process Integration
- Shotgun Metagenomics Pipeline (shotgun-metagenomics)
- 16S rRNA Microbiome Analysis (16s-microbiome-analysis)

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