annotation-helixer/main
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Run on GalaxyThis workflow allows you to annotate a genome with Helixer and evaluate the quality of the annotation using BUSCO and Genome Annotation statistics. GFFRead is also used to predict protein sequences derived from this annotation, and BUSCO and OMArk are used to assess proteome quality.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Genome sequence | #main/Genome sequence | Input dataset containing genomic sequences in FASTA format |
|
Steps
| ID | Name | Description |
|---|---|---|
| 1 | Helixer | Helixer tool for genomic annotation toolshed.g2.bx.psu.edu/repos/genouest/helixer/helixer/0.3.3+galaxy1 |
| 2 | Busco on genome | Completeness assessment of the genome using the Busco tool toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0 |
| 3 | Gffread | Converts GFF files to other formats, such as FASTA toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.4+galaxy0 |
| 4 | Genome annotation statistics | Generates statistics and graphs for genome annotation toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4 |
| 5 | JBrowse | JBrowse toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 |
| 6 | Busco on protein | Completeness assessment of the genome using the Busco tool toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0 |
| 7 | OMArk | OMArk toolshed.g2.bx.psu.edu/repos/iuc/omark/omark/0.3.0+galaxy2 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| busco gff genome | #main/busco gff genome | n/a |
|
| busco gff peptides | #main/busco gff peptides | n/a |
|
| busco missing genome | #main/busco missing genome | n/a |
|
| busco missing peptides | #main/busco missing peptides | n/a |
|
| busco sum genome | #main/busco sum genome | n/a |
|
| busco sum peptides | #main/busco sum peptides | n/a |
|
| busco table genome | #main/busco table genome | n/a |
|
| busco table peptides | #main/busco table peptides | n/a |
|
| gffread peptides | #main/gffread peptides | n/a |
|
| graphs | #main/graphs | n/a |
|
| helixer output | #main/helixer output | n/a |
|
| omark detail sum | #main/omark detail sum | n/a |
|
| omark sum | #main/omark sum | n/a |
|
| output | #main/output | n/a |
|
| summary | #main/summary | n/a |
|
| summary image genome | #main/summary image genome | n/a |
|
| summary image peptides | #main/summary image peptides | n/a |
|
Version History
v0.1 (earliest) Created 25th Jan 2025 at 03:02 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.18cc0bc4
Creators and SubmitterViews: 2931 Downloads: 3101 Runs: 0
Created: 25th Jan 2025 at 03:01
Last updated: 18th Aug 2025 at 16:40
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Teams: Intergalactic Workflow Commission (IWC), Vertebrate Genomes Pipelines in Galaxy, nf-core
Organizations: Bots, European Galaxy Team
https://orcid.org/0009-0001-4920-9951
Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.
- Accessible: Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface.
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Teams: Galaxy Training Network, usegalaxy-eu, Intergalactic Workflow Commission (IWC)
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ELIXIR is an intergovernmental organisation that brings together life science resources from across Europe. These resources include databases, software tools, training materials, cloud storage and supercomputers.
The goal of ELIXIR is to coordinate these resources so that they form a single infrastructure. This infrastructure makes it easier for scientists to find and share data, exchange expertise, and agree on best practices. Ultimately, it will help them gain new insights into how living ...
Teams: ELIXIR Training, FAIR Computational Workflows, EuroScienceGateway, BY-COVID (general), ELIXIR Tools platform, ELIXIR Metabolomics
Web page: https://elixir-europe.org/
EuroScienceGateway will leverage a distributed computing network across 13 European countries, accessible via 6 national, user-friendly web portals, facilitating access to compute and storage infrastructures across Europe as well as to data, tools, workflows and services that can be customized to suit researchers’ needs.EuroScienceGateway will deliver a robust, scalable, seamlessly integrated open infrastructure for data-driven research, contributing an innovative and customizable service for ...
Space: ELIXIR
Public web page: https://eurosciencegateway.eu/
Start date: 1st Oct 2022
End date: 31st Aug 2025
The Intergalactic Workflow Commission releases vetted analysis pipelines for the Galaxy platform.
You can contribute too!
Space: Galaxy
Public web page: https://iwc.galaxyproject.org/
Collection of workflows used or developed by the EuroScienceGateway project.
Maintainers: Stian Soiland-Reyes, Paul De Geest, Eli Chadwick, Armin Dadras
Number of items: 48
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