Generates a highly customizable abundance table from multiple reports, with support for different metrics and formatting options.
kraut make-table [OPTIONS] INPUT_FILES...
| Argument | Type | Description |
|---|---|---|
INPUT_FILES... |
PATH | Required. One or more Kraken report files. |
| Option | Short | Type | Description |
|---|---|---|---|
--output |
-o |
PATH | Output file (default: stdout). |
--metric |
-m |
TEXT | Metric: LVL (taxon-specific), TOT (cumulative), PERCENTAGE (default: TOT). |
--rank |
-r |
TEXT | Taxonomic rank (K, P, C, O, F, G, S, ALL) (default: S). |
--rank-prefix |
-p |
Add rank prefix to names (e.g., s__Species). |
|
--taxid |
Use TaxID instead of taxon name as the identifier. | ||
--no-unclassified |
Exclude unclassified reads. | ||
--min-perc |
FLOAT | Remove rows where no sample reaches this % abundance (default: 0.0). |
kraut make-table data/*.krep -o species_table.tsv
This is the standard command for merging multiple Kraken reports into one comparison table.
kraut make-table data/*.krep -r G -p -m PERCENTAGE -o genus_table.tsv
Keep only taxa that reach at least 0.5% abundance in at least one sample:
kraut make-table data/*.krep --min-perc 0.5 -o filtered_table.tsv