Performes assembly of input short reads.
Parameters in GUI
| Parameter | Description | Default value |
|---|---|---|
| Output directory | Directory to save Spades output files. | |
| Dataset type | Input dataset type. | Multi Cell |
| Running mode | Running mode. | Error correction and assembly |
| K-mers | k-mer sizes (-k). | auto |
| Number of threads | Number of threads (-t). | 16 |
| Memory limit (Gb) | Memory limit (-m). | 250 |
Parameters in Workflow File
Type: spades-id
| Parameter | Parameter in the GUI | Type |
|---|---|---|
| output-dir | Output directory | string |
| dataset-type | Dataset type | string |
| running-mode | Running mode | string |
| k-mer | K-mers | numeric |
| threads | Number of threads | numeric |
| memlimit | Memory limit (Gb) | numeric |
Input/Output Ports
The element has 1 input port:
Name in GUI: Spades data
Name in Workflow File: in-data
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| URL of a file with right pair reads | url | string |
| URL of a file with reads | url | string |
And 1 output port:
Name in GUI: SPAdes output data
Name in Workflow File: out-data
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| ScaffoIds URL | url | string |