SYNOPSIS

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.