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  • Assemble Genomes with SPAdes Element

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Performes assembly of input short reads.

Parameters in GUI

ParameterDescriptionDefault value
Output directoryDirectory to save Spades output files. 
Dataset typeInput dataset type.Multi Cell
Running modeRunning mode.Error correction and assembly
K-mersk-mer sizes (-k).auto
Number of threadsNumber of threads (-t).16
Memory limit (Gb)Memory limit (-m).250

Parameters in Workflow File

Type: spades-id

ParameterParameter in the GUIType
output-dirOutput directory


dataset-typeDataset typestring
running-modeRunning modestring
threadsNumber of threadsnumeric
memlimitMemory limit (Gb)numeric

Input/Output Ports

The element has 1 input port:

Name in GUI: Spades data

Name in Workflow File: in-data


Slot In GUISlot in Workflow FileType
URL of a file with right pair readsurlstring
URL of a file with readsurlstring

And 1 output port:

Name in GUI: SPAdes output data

Name in Workflow File: out-data


Slot In GUISlot in Workflow FileType
ScaffoIds URLurlstring