Funannotate 1.0
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Run on GalaxyStructural and functional genome annotation with Funannotate
Associated Tutorial
This workflows is part of the tutorial Genome annotation with Funannotate, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Anthony Bretaudeau
Tutorial Author(s): Anthony Bretaudeau
Tutorial Contributor(s): Alexandre Cormier, Laura Leroi, Erwan Corre, Stéphanie Robin, Helena Rasche, Cristóbal Gallardo, Anthony Bretaudeau, Björn Grüning, Jonathan Kreplak, Saskia Hiltemann, Bérénice Batut, Simon Bray
Funder(s): ELIXIR Europe
Grants(s): Gallantries: Bridging Training Communities in Life Science, Environment and Health, EuroScienceGateway
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) |
|
| 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/) |
|
| 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 |
|
| 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 |
|
| Busco image | #main/Busco image | n/a |
|
| Busco summary | #main/Busco summary | n/a |
|
| Final annotation (CDS sequences) | #main/Final annotation (CDS sequences) | n/a |
|
| Final annotation (GFF3) | #main/Final annotation (GFF3) | n/a |
|
| Final annotation (genbank) | #main/Final annotation (genbank) | n/a |
|
| Final annotation (mRNA sequences) | #main/Final annotation (mRNA sequences) | n/a |
|
| Final annotation (protein sequences) | #main/Final annotation (protein sequences) | n/a |
|
| Funannotate compare report | #main/Funannotate compare report | n/a |
|
| JBrowse | #main/JBrowse | n/a |
|
| 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 |
|
| _anonymous_output_5 | #main/_anonymous_output_5 | n/a |
|
Version History
1.0
Creators and Submitter
Views: 571 Downloads: 73 Runs: 0
Created: 2nd Jun 2025 at 10:57
Last updated: 28th Jul 2025 at 10:56
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