Extract Coverage from Assembly
This workflow sample extracts coverage and/or base counts from input assemblies. It supports multiple input assemblies and produces a tab-delimited plain text output for each of them. Coverage values are filtered based on the provided threshold parameter.
How to Use This Sample
If you haven’t used workflow samples in UGENE before, refer to the How to Use Sample Workflows section of the documentation.
Workflow Sample Location
The workflow sample “Extract Coverage from Assembly” is available in the “NGS” section of the Workflow Designer samples.
Workflow Image
The workflow appears as follows:
Workflow Wizard
The wizard consists of 3 pages:
1. Input Assembly(ies)
On this page, input one or more assembly files.
2. Extract Parameters
Configure the extraction parameters:
| Parameter | Description |
|---|---|
| Format | Output file format (tab-delimited plain text). |
| Export | Type of data to export: coverage or base counts. |
| Threshold | Minimum coverage value to include in the output. |
3. Output Data
On this page, select the destination for the output file.
Output Example
Each output file will contain coverage data per base or region, based on the selected export mode and threshold.