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kraken - assigning taxonomic labels to short DNA sequences


kraken [options] <filename(s)>


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

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

Input is FASTA format

Input is FASTQ format

Input is gzip compressed

Input is bzip2 compressed

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

Print no Kraken output for unclassified sequences

Loads DB into memory before classification

The two filenames provided are paired-end reads

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

--help Print this message

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.

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