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KRAKEN(1) User Commands KRAKEN(1)


kraken - assigning taxonomic labels to short DNA sequences


kraken [options] <filename(s)>


Name for Kraken DB (default: none)
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)
In quick op., number of hits req'd for classification NOTE: this is ignored if --quick is not specified
Print unclassified sequences to filename
Print classified sequences to 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