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This is the command kraken that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator



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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