kraut

A python package for parsing, merging, and analyzing Kraken2 output files.

Installation

From PyPI:

pip install krautils

From a local checkout:

pip install .

For developer's dependencies:

pip install .[dev]
pytest

Command

kraut parses, filters, merges, tabulates, splits, and plots Kraken2 reports.

• single-report: filter or reformat one Kraken report.
• make-table: build a configurable multi-sample abundance table.
• make-mpa-table: merge MetaPhlAn profiles into a multi-sample abundance table.
• table-summary: summarize a table produced by make-table.
• ma-export: export reports for MicrobiomeAnalyst as counts, taxonomy, metadata, and tree files.
• alpha: calculate alpha diversity from Kraken or Bracken reports.
• beta: calculate beta diversity distance matrices and heatmap/PCA plots.
• dendrogram: plot hierarchical clustering dendrograms from beta distances.
• split-combine-table: split a KrakenTools combined table into ALL/LVL tables.
• plot-single: plot one sample as an HTML or static composition chart.
• plot-multi: plot multiple samples as an HTML or static stacked/bubble chart.

kraut alpha reports/*.tsv -o alpha.tsv -p alpha.html --metrics core --add-metrics chao1,ace
kraut beta reports/*.tsv -o beta.tsv --plot beta.html --pca beta_pca.html
kraut dendrogram reports/*.tsv -o dendrogram.html --distance braycurtis --clustering ward
kraut ma-export reports/*.tsv -o microbiomeanalyst --metadata metadata.tsv --metadata-sample-col Sample
kraut make-mpa-table profiles/*_profile.tsv -o metaphlan_species.tsv --keep-taxid --drop-unclassified --normalise

ma-export writes counts.csv, taxonomy.csv, metadata.csv, and tree.nwk. It uses taxon-specific counts by default (--metric LVL); use --metric TOT for cumulative clade counts.

Example plots:

License

This project is licensed under the MIT License. See LICENSE.