kraut
Kraut Overview
| Overview | Installation | Commands |
Kraut (packaged as krautils) is a Python toolset for parsing, merging, and analyzing Kraken2 taxonomic reports. It provides a suite of commands to handle single reports, merge multiple datasets, generate abundance tables, calculate alpha and beta diversity, and create interactive or static visualizations.
Key Features
- Standardization: Convert and filter Kraken2 reports into consistent formats.
- Aggregation: Merge multiple samples into a single comparative table.
- Diversity Analysis: Calculate alpha diversity metrics (Shannon, Simpson, etc.) and beta diversity distances directly from reports.
- Visualization: Generate high-quality composition plots (stacked bars, bubble charts) in HTML or static formats (PNG, SVG, PDF).
- Flexibility: Support for both cumulative (TOT) and taxon-specific (LVL) metrics.
Example Visualizations
Multi-sample Stacked Bar Chart
Single-sample Composition
Bubble Chart
