bactopia-kraken-bracken-summary
Update the Bracken abundances with unclassified counts.
Usage
bactopia-kraken-bracken-summary PREFIX KRAKEN2_REPORT BRACKEN_REPORT BRACKEN_ABUNDANCES [OPTIONS]
Arguments
| Argument | Type | Required | Description |
|---|---|---|---|
PREFIX | STRING | Yes | Prefix to use for output files. |
KRAKEN2_REPORT | STRING | Yes | The Kraken2 report. |
BRACKEN_REPORT | STRING | Yes | The Bracken updated Kraken2 report. |
BRACKEN_ABUNDANCES | STRING | Yes | The Bracken output with abundances. |
Options
| Option | Type | Default | Description |
|---|---|---|---|
--version, -V | BOOL | false | Show the version and exit. |
--max_secondary_percent | FLOAT | 0.01 | The maximum percent abundance for the secondary species, if exceeded, sample will remain unclassified. |