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
Element type: kraken-classify
Parameters
Parameter | Description | Defaultvalue | Parameter in Workflow File | Type |
---|---|---|---|---|
Input data | To classify single-end (SE) reads or contigs, received by reads de novo assembly, set this parameter to "SE reads or contigs". | 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. | False | quick-operation | bool |
Load database into memory | Load the Kraken database into RAM (--preload). | True | preload | bool |
Number of threads | Use multiple threads (--threads). | 8 | threads | number |
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
threads
Number of threads
number
Load database into memory
bool
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:
SlotInGUI | Slot in Workflow File | Type |
---|---|---|
Input URL | url | string |
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:
SlotInGUI | Slot in Workflow File | Type |
---|---|---|
Taxonomy classification data | tax-data | tax-classification |