Genome annotation with Funannotate Version 1
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Run on GalaxyStructural and functional genome annotation with Funannotate
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Alternate annotation gbk | #main/Alternate annotation gbk | The genbank output of an alternate annotation (for comparison) |
|
| Alternate annotation gff3 | #main/Alternate annotation gff3 | The gff3 output of an alternate annotation (for comparison) |
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| Genome assembly | #main/Genome assembly | The genome sequence that you wish to annotate, in fasta format. It needs to be soft masked beforehand. |
|
| NCBI submission template | #main/NCBI submission template | A submission template retrieved from NCBI (generate it on https://submit.ncbi.nlm.nih.gov/genbank/template/submission/) |
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| Protein evidence sequences | #main/Protein evidence sequences | Some protein sequences to align on the genome to help annotation |
|
| RNASeq reads forward | #main/RNASeq reads forward | Some RNASeq data, forward reads, in fastq format |
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| RNASeq reads reverse | #main/RNASeq reads reverse | Some RNASeq data, reverse reads, in fastq format |
|
Steps
| ID | Name | Description |
|---|---|---|
| 7 | RNA STAR | toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy3 |
| 8 | Funannotate predict annotation | toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.15+galaxy0 |
| 9 | eggNOG Mapper | toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy3 |
| 10 | InterProScan | toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3 |
| 11 | Funannotate functional | toolshed.g2.bx.psu.edu/repos/iuc/funannotate_annotate/funannotate_annotate/1.8.15+galaxy0 |
| 12 | JBrowse | toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 |
| 13 | Funannotate compare | toolshed.g2.bx.psu.edu/repos/iuc/funannotate_compare/funannotate_compare/1.8.15+galaxy0 |
| 14 | AEGeAn ParsEval | toolshed.g2.bx.psu.edu/repos/iuc/aegean_parseval/aegean_parseval/0.16.0 |
| 15 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| AEGeAN report | #main/AEGeAN report | n/a |
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| Busco image | #main/Busco image | n/a |
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| Busco summary | #main/Busco summary | n/a |
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| Final annotation (CDS sequences) | #main/Final annotation (CDS sequences) | n/a |
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| Final annotation (GFF3) | #main/Final annotation (GFF3) | n/a |
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| Final annotation (genbank) | #main/Final annotation (genbank) | n/a |
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| Final annotation (mRNA sequences) | #main/Final annotation (mRNA sequences) | n/a |
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| Final annotation (protein sequences) | #main/Final annotation (protein sequences) | n/a |
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| Funannotate compare report | #main/Funannotate compare report | n/a |
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| JBrowse | #main/JBrowse | n/a |
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| Mapped RNASeq | #main/Mapped RNASeq | n/a |
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| _anonymous_output_1 | #main/_anonymous_output_1 | n/a |
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| _anonymous_output_2 | #main/_anonymous_output_2 | n/a |
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| _anonymous_output_3 | #main/_anonymous_output_3 | n/a |
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| _anonymous_output_4 | #main/_anonymous_output_4 | n/a |
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| _anonymous_output_5 | #main/_anonymous_output_5 | n/a |
|
Version History
Version 1 (earliest) Created 15th Feb 2024 at 11:39 by Paul De Geest
Initial commit
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Creators and SubmitterViews: 4921 Downloads: 563 Runs: 3
Created: 15th Feb 2024 at 11:39
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Teams: EuroScienceGateway, ELIXIR Belgium
Organizations: ELIXIR Belgium
https://orcid.org/0000-0002-8940-4946
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
Abstract (Expand)
Authors: Stian Soiland-Reyes, Björn Grüning, Paul De Geest
Date Published: 29th Feb 2024
Publication Type: Tech report
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
Tags: Not specified
