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Kraken is a taxonomic sequence classifier that assigns taxonomic labels to short DNA reads. It does this by examining the k-mers within a read and querying a database with those.

Element type: kraken-classify

Parameters

ParameterDescriptionDefaultvalueParameter in Workflow FileType
Input data

To classify single-end (SE) reads or contigs, received by reads de novo assembly, set this parameter to "SE reads or contigs".
To classify paired-end (PE) reads, set the value to "PE reads".
One or two slots of the input port are used depending on the value of the parameter. Pass URL(s) to data to these slots.
The input files should be in FASTA or FASTQ formats.

 SE reads or contigs

input-data

string

Database

A path to the folder with the Kraken database files.


database

string

Quick operation

Stop classification of an input read after the certain number of hits.
The value can be specified in the "Minimum number of hits" parameter.

False

quick-operation

bool

Load database into memory

Load the Kraken database into RAM (--preload).
This can be useful to improve the speed. The database size should be less than the RAM size.
The other option to improve the speed is to store the database on ramdisk. Set this parameter to "False" in this case.

True

preload

bool

Number of threads

Use multiple threads (--threads).

8

threads

number

Output file

Specify the output file name.

auto

output-url

string

Input/Output Ports

The element has 1 input port:

Name in GUI: Input sequences: 

URL(s) to FASTQ or FASTA file(s) should be provided. In case of SE reads or contigs use the "Input URL 1" slot only.

In case of PE reads input "left" reads to "Input URL 1", "right" reads to "Input URL 2". See also the "Input data" parameter of the element.

Name in Workflow File: in

Slots:

SlotInGUISlot in Workflow FileType
Input URLurlstring

The element has 1 output port:

Name in GUI: Kraken Classification


A map of sequence names with the associated taxonomy IDs, classified by Kraken.

Name in Workflow File: out

Slots:

SlotInGUISlot in Workflow FileType
Taxonomy classification data

tax-data

tax-classification


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