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KRAKEN(1) User Commands KRAKEN(1)


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

September 2015 kraken 0.10.5~beta