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GenomeQC pipeline integrates various quantitative measures to characterize genome assemblies and annotations. We have used the containerized version of GenomeQC to create an app in Discovery Environment.
Launch GenomeQC app
- Login to the Discovery Environment.
- CLick on "Apps" tab in the Discovery Enviornment and search for "GenomeQC".
- Click on the app icon.
- Change the name of the analysis and output folder as needed or leave for defaults.
- Under "Inputs" provide the genome annotation, transcript and BUSCO dataset. Use the example dataset or provide your own dataset.
- Under "Resource Requirements" request resources as needed or leave for defaults
- Click Launch Analysis. You will receive a notification that the job has been submitted and running. Click on 'Access your analysis here' link.
- Repeat the same steps for benchmarking with gold-standard dataset.
Prerequisites
Downloads, access, and services
In order to complete this tutorial you will need access to the following services/software
| Prerequisite | Preparation/Notes | Link/Download |
|---|---|---|
| CyVerse account | You will need a CyVerse account to complete this exercise | |CyVerse User Portal| |
| JetStream access | You must have access to JetStream | Atmosphere Image |
| Cyberduck | Standalone software for upload/download to Data Store | Download Cyberduck |
Platform(s)
We will use the following CyVerse platform(s):
| Platform | Interface | Link | Platform Documentation | Quick Start |
|---|---|---|---|---|
| Data Store | GUI/Command line | |Data Store| | |Data Store Manual| | |Data Store Guide| |
| Discovery Environment | Web/Point-and-click | |Discovery Environment| | |DE Manual| | |Discovery Environment Guide| |
Application(s) used ..
#### Comment: these tables are examples, delete whatever is unnecessary ####
Discovery Environment App(s):
| App name | Version | Description | App link | Notes/other links |
|---|---|---|---|---|
| GenomeQC_annotation | 1.0 | Genome Annotation Quality | DE Application URL | Original App Documentation |
Input and example data
In order to complete this tutorial you will need to have the following inputs prepared
| Input File(s) | Format | Preparation/Notes | Example Data |
|---|---|---|---|
| Genome annotation, transcript file, BUSCO dataset | GFF, FASTA | BUSCO sample datasets Community Data -> iplantcollaborative -> example_data -> BUSCO.sample.data | Community Data -> iplantcollaborative -> example_data -> genomeqc_annotation |
Fix or improve this documentation
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