Provided by: kraken_0.10.5~beta-2_amd64
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.