NAME

       kraken2 - assigning taxonomic labels to short DNA sequences

SYNOPSIS

       kraken2 [options] <filename(s)>

OPTIONS

       --db NAME
              Name for Kraken 2 DB (default: none)

       --threads NUM
              Number of threads (default: 1)

       --quick
              Quick operation (use first hit or hits)

       --unclassified-out FILENAME
              Print unclassified sequences to filename

       --classified-out FILENAME
              Print classified sequences to filename

       --output FILENAME
              Print output to filename (default: stdout); "-" will suppress normal output

       --confidence FLOAT
              Confidence score threshold (default: 0.0); must be in [0, 1].

       --minimum-base-quality NUM
              Minimum base quality used in classification (def: 0, only effective with FASTQ input).

       --report FILENAME
              Print a report with aggregrate counts/clade to file

       --use-mpa-style
              With --report, format report output like Kraken 1's kraken-mpa-report

       --report-zero-counts
              With --report, report counts for ALL taxa, even if counts are zero

       --memory-mapping
              Avoids loading database into RAM

       --paired
              The filenames provided have paired-end reads

       --use-names
              Print scientific names instead of just taxids

       --gzip-compressed
              Input files are compressed with gzip

       --bzip2-compressed
              Input files are compressed with bzip2

       --help Print this message

       --version
              Print version information

       If  none  of the *-compressed flags are specified, and the filename provided is a regular file, automatic
       format detection is attempted.

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage
       of the program.

kraken2 2.0.7~beta                                 March 2019                                         KRAKEN2(1)