Splits a KrakenTools combined table into two separate tables: one with all taxonomic information (ALL) and one filtered by a specific rank (LVL), while cleaning up headers for better compatibility with downstream tools.
kraut split-combine-table [OPTIONS]
| Option | Short | Type | Description |
|---|---|---|---|
--input |
-i |
PATH | Required. Input table in KrakenTools combined format. |
--output |
-o |
TEXT | Required. Output basename (will create _all.tsv and _lvl.tsv). |
--rank |
-r |
TEXT | Filter by rank code (e.g., S). |
--taxid |
Use TaxID as the first column instead of the taxon name. |
kraut split-combine-table -i combined_table.txt -o split_table -r S
This will generate split_table_all.tsv and split_table_lvl.tsv.
kraut split-combine-table -i combined_table.txt -o taxid_output --taxid