Workflow Designer Documentation v. 33
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  • Classify Sequences with Kraken
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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.

Parameters in GUI

 

ParameterDescriptionDefaultvalue
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
Database

A path to the folder with the Kraken database files.

 
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
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
Number of threads

Use multiple threads (--threads).

8
Output file

Specify the output file name.

auto

Parameters in Workflow File

Type: kraken-classify

Parameter

Parameter in the GUI

Type

input-data

Input data

string

database

Database

string

quick-operation

Quick operation

bool

preload

Load database into memory

bool

threads

Number of threads

number

output-url

Output file

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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