Parses a Kraken report and prints it in text format, optionally filtering by abundance or taxonomic level.
kraut single-report [OPTIONS]
| Option | Short | Type | Description |
|---|---|---|---|
--input |
-i |
PATH | Required. Input Kraken report file (KREP). |
--output |
-o |
PATH | Output file (default: stdout). |
--min-fract |
-m |
FLOAT | Minimum fraction of reads to keep a taxon (default: 0.0). |
--min-count |
-c |
INTEGER | Minimum count of reads to keep a taxon (default: 0). |
--min-level |
-l |
TEXT | Minimum level to keep (K, P, C, O, F, G, S). |
--max-level |
-L |
TEXT | Maximum level to keep (e.g., do not print below Species). |
kraut single-report -i sample.krep -o output.txt
Keep only taxa with at least 1% abundance and at least 100 reads:
kraut single-report -i sample.krep -m 0.01 -c 100
Only show results from Phylum to Genus:
kraut single-report -i sample.krep -l P -L G