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Parameter | Description | Defaultvalue |
---|---|---|
Input data | To classify single-end (SE) reads or scaffoldscontigs, received by reads de novo assembly, set this parameter to "SE reads or scaffoldscontigs". | SE reads or scaffoldscontigs |
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. | False |
Load database into memory | Load the Kraken database into RAM (--preload). | True |
Number of threads | Use multiple threads (--threads). | 8 |
Output file | Specify the output file name. | auto |
Parameters in Workflow File
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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 scaffolds 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 |