Funannotate
1.0

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Workflow Type: Galaxy

Structural and functional genome annotation with Funannotate

Associated Tutorial

This workflows is part of the tutorial Funannotate, available in the GTN

Features

Thanks to...

Tutorial Author(s): Anthony Bretaudeau

Tutorial Contributor(s): Alexandre Cormier, Laura Leroi, Erwan Corre, Stéphanie Robin

Workflow Author(s): Anthony Bretaudeau

Funder(s): Gallantries: Bridging Training Communities in Life Science, Environment and Health, EuroScienceGateway

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1202?version=1

Inputs

ID Name Description Type
Alternate annotation gbk #main/Alternate annotation gbk The genbank output of an alternate annotation (for comparison)
  • File
Alternate annotation gff3 #main/Alternate annotation gff3 The gff3 output of an alternate annotation (for comparison)
  • File
Genome assembly #main/Genome assembly The genome sequence that you wish to annotate, in fasta format. It needs to be soft masked beforehand.
  • File
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/)
  • File
Protein evidence sequences #main/Protein evidence sequences Some protein sequences to align on the genome to help annotation
  • File
RNASeq reads forward #main/RNASeq reads forward Some RNASeq data, forward reads, in fastq format
  • File
RNASeq reads reverse #main/RNASeq reads reverse Some RNASeq data, reverse reads, in fastq format
  • File

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
  • File
Busco image #main/Busco image n/a
  • File
Busco summary #main/Busco summary n/a
  • File
Final annotation (CDS sequences) #main/Final annotation (CDS sequences) n/a
  • File
Final annotation (GFF3) #main/Final annotation (GFF3) n/a
  • File
Final annotation (genbank) #main/Final annotation (genbank) n/a
  • File
Final annotation (mRNA sequences) #main/Final annotation (mRNA sequences) n/a
  • File
Final annotation (protein sequences) #main/Final annotation (protein sequences) n/a
  • File
Funannotate compare report #main/Funannotate compare report n/a
  • File
JBrowse #main/JBrowse n/a
  • File
Mapped RNASeq #main/Mapped RNASeq n/a
  • File
_anonymous_output_1 #main/_anonymous_output_1 n/a
  • File
_anonymous_output_2 #main/_anonymous_output_2 n/a
  • File
_anonymous_output_3 #main/_anonymous_output_3 n/a
  • File
_anonymous_output_4 #main/_anonymous_output_4 n/a
  • File
_anonymous_output_5 #main/_anonymous_output_5 n/a
  • File

Version History

1.0 (earliest) Created 25th Jun 2024 at 11:09 by Helena Rasche

Added/updated 4 files


Open master 9dfe055
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tools
STAR
funannotate
eggNOG-mapper v2
InterProScan (EBI)
JBrowse
GAEVAL
BUSCO
License
GNU General Public License v3.0 or later
Activity

Views: 457   Downloads: 100

Created: 25th Jun 2024 at 11:09

Last updated: 25th Jun 2024 at 11:09

help Attributions

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Total size: 201 KB
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