kraken(1) 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.