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kraken - Online in the Cloud

Run kraken in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

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

PROGRAM:

NAME


kraken - assigning taxonomic labels to short DNA sequences

SYNOPSIS


kraken [options] <filename(s)>

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.

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