Extract Coverage from Assembly Element
This workflow element extracts coverage and/or base counts from incoming assembly data.
Element type: extract-assembly-coverage
Parameters
| Parameter | Description | Default Value | Parameter in Workflow File | Type |
|---|---|---|---|---|
| Output file | Path to the output data file. If this is set, the slot Location will not be used. | assembly_coverage.txt | url-out | string |
| Export | Type of data to export: coverage or base-count. | coverage | export-type | string |
| Threshold | Minimum coverage value to include in the output. | 1 | threshold | numeric |
Input/Output Ports
Input Port
| Name in GUI | Name in Workflow File | Slot | Slot in Workflow File | Type |
|---|---|---|---|---|
in-assembly | in-assembly | Assembly data | assembly | assembly |
Output Port
(None defined directly in the current schema – output is handled via the file path parameter url-out.)
Example
To extract base coverage from a single assembly file:
ugene workflow run \
--element extract-assembly-coverage \
--url-out ./coverage.txt \
--export-type coverage \
--threshold 5
This will output coverage data for all positions with at least 5x coverage.