GenomeQC App in the Discovery Environment¶
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 |
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