Commands
Kraut provides several subcommands for different tasks. Click on a command name to see its syntax and examples.
- single-report: Filter or reformat a single 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.csv, taxonomy.csv, metadata.csv, and tree.nwk.
- alpha: Calculate alpha diversity metrics.
- beta: Calculate beta diversity distance matrices and ordination plots.
- dendrogram: Plot hierarchical clustering dendrograms.
- plot-single: Plot composition for one sample.
- plot-multi: Plot composition across multiple samples.
- split-combine-table: Split a KrakenTools combined table into ALL/LVL tables.