kraken2-taxonomic-classifier

name	kraken2-taxonomic-classifier
description	Kraken2 taxonomic classification skill for rapid metagenomic read assignment
allowed-tools	["Read","Write","Glob","Grep","Edit","WebFetch","WebSearch","Bash"]
metadata	{"version":"1.0","category":"bioinformatics","tags":["metagenomics","taxonomy","classification","kraken"]}
graph	{"domains":["domain:bioinformatics"],"specializations":["specialization:biomedical-informatics"],"skillAreas":["skill-area:graph-algorithms","skill-area:python-data-pipelines","skill-area:data-analysis"],"workflows":["workflow:experiment-design"],"roles":["role:research-engineer","role:biomedical-engineer"]}

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)