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.