list-reads
Lists read names from a Kraken raw output file that match a taxon selection.
Syntax
kraut list-reads [OPTIONS] RAW_OUTPUT
Arguments
| Argument |
Type |
Description |
RAW_OUTPUT |
PATH |
Required. A Kraken raw output TSV. |
Options
| Option |
Short |
Type |
Description |
--taxon |
-t |
INTEGER |
TaxID to match; repeatable. |
--children |
|
|
Include each selected taxon and its descendants (requires --report). |
--report |
-r |
PATH |
Kraken report TSV; required with --children. |
--unclassified |
|
|
Include unclassified reads. |
--invert |
-v |
|
Output reads that do not match the selection. |
--output |
-o |
PATH |
Output file (default: stdout). |
Examples
Reads assigned to one or more taxa
kraut list-reads sample.out --taxon 562 --taxon 208964
Reads for a taxon and its descendants
kraut list-reads sample.out --taxon 2 --children --report sample.krep
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