ranks
Profiles the reads assigned at each canonical taxonomic rank (U, R, D, K, P, C, O, F, G, S) for one or more Kraken or Bracken reports.
Syntax
kraut ranks [OPTIONS] INPUT_FILES...
Arguments
| Argument |
Type |
Description |
INPUT_FILES... |
PATH |
Required. One or more Kraken or Bracken report files. |
Options
| Option |
Short |
Type |
Description |
--output |
-o |
PATH |
Output TSV file (default: stdout). |
--counts |
|
|
Print raw read counts instead of percentages. |
--plot |
-p |
PATH |
Write a stacked rank-composition bar chart (.html, .png, .pdf, .svg). |
Examples
Rank composition table
kraut ranks reports/*.krep -o ranks.tsv
Read counts and a plot
kraut ranks reports/*.krep --counts -p ranks_plot.png
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