NAME

       kraken - assigning taxonomic labels to short DNA sequences

SYNOPSIS

       kraken [options] <filename(s)>

OPTIONS

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

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

       --fasta-input
              Input is FASTA format

       --fastq-input
              Input is FASTQ format

       --gzip-compressed
              Input is gzip compressed

       --bzip2-compressed
              Input is bzip2 compressed

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

       --min-hits NUM
              In  quick  op.,  number  of  hits req'd for classification NOTE: this is ignored if
              --quick is not specified

       --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

       --only-classified-output
              Print no Kraken output for unclassified sequences

       --preload
              Loads DB into memory before classification

       --paired
              The two filenames provided are paired-end reads

       --check-names
              Ensure each pair of reads have  names  that  agree  with  each  other;  ignored  if
              --paired is not specified

       --help Print this message

       --version
              Print version information

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