What it does

After running Kraken, Kraken2, or KrakenUniq, users may use the kreport2krona.py program to convert the report file to a tabular format suitable for input into Krona.

Example usage

kraken2 --db KRAKEN2DB --threads THREADNUM --report MYSAMPLE.KREPORT     --paired SAMPLE_1.FASTA SAMPLE_2.FASTA > MYSAMPLE.KRAKEN2
kreport2krona.py --report MYSAMPLE.KREPORT --output MYSAMPLE.krona
ktImportText MYSAMPLE.krona -o MYSAMPLE.krona.html

Command-line arguments

The following command-line usage corresponds with the Galaxy wrapper parameters:

usage: kreport2krona.py [-h] -r R_FILE -o O_FILE [--intermediate-ranks] [--no-intermediate-ranks]

optional arguments:
    -h, --help            show this help message and exit
    -r R_FILE, --report-file R_FILE, --report R_FILE
                            Input kraken report file for converting
    -o O_FILE, --output O_FILE
                            Output krona-report file name
    --intermediate-ranks  Include non-traditional taxonomic ranks in output
    --no-intermediate-ranks
                            Do not include non-traditional taxonomic ranks in output [default: no intermediate ranks]

More Information

Author: Jennifer Lu

See the online documentation

Galaxy Wrapper Development

Author: Jeremy Volkening