krautils 0.3.0

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

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.
• merge-reports: merge reports into a simple comparison table.
• make-table: build a configurable multi-sample abundance table.
• alpha: calculate alpha diversity from Kraken or Bracken reports.
• 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

Example plots: