Calculates alpha diversity metrics for Kraken or Bracken report files and optionally generates a visualization.
kraut alpha [OPTIONS] INPUT_FILES...
| Argument | Type | Description |
|---|---|---|
INPUT_FILES... |
PATH | Required. One or more Kraken or Bracken report files. |
| Option | Short | Type | Description |
|---|---|---|---|
--output-table |
-o |
PATH | Output alpha diversity table (default: alpha.tsv). |
--plot |
-p |
PATH | Optional plot file (.html, .png, .svg, .pdf). |
--rank |
-r |
TEXT | Taxonomic rank to use (default: S). |
--metric |
-m |
TEXT | Abundance metric: TOT (cumulative) or LVL (taxon-specific) (default: TOT). |
--metrics |
TEXT | Alpha metric preset or comma-separated list (default: core). |
|
--add-metrics |
TEXT | Comma-separated additional alpha metrics to append. | |
--include-unclassified |
Include unclassified reads as a feature in calculations. | ||
--min-perc |
FLOAT | Remove taxa where no sample reaches this % abundance (default: 0.0). |
kraut alpha reports/*.krep -o diversity_stats.tsv
Calculate Shannon and Simpson indices and save a PNG plot:
kraut alpha reports/*.krep --metrics "shannon,simpson" -p alpha_plot.png
kraut alpha bracken_outputs/*.brep -r G -o genus_alpha.tsv