annotation-braker3/main
v0.1

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Workflow Type: Galaxy

This workflow performs genome annotation using Braker3 and evaluates the quality of the annotation with BUSCO and genome annotation statistics.

SEEK ID: https://workflowhub.eu/workflows/2029?version=1

Inputs

ID Name Description Type
Alignments from RNA-seq #main/Alignments from RNA-seq Alignments from RNA-seq
  • File
BUSCO database #main/BUSCO database BUSCO database
  • string
BUSCO lineage #main/BUSCO lineage BUSCO lineage
  • string
Fungus genome #main/Fungus genome If your genome is a fungus, would you like to use the --fungus parameter for Braker3 analyses?
  • boolean
Include BUSCO #main/Include BUSCO By selecting yes, BUSCO analyses will be performed on the genome and predicted protein sequences.
  • boolean
Protein sequences #main/Protein sequences Protein sequences
  • File
Soft masked Genome sequence #main/Soft masked Genome sequence Genome sequence
  • File

Steps

ID Name Description
7 BUSCO on the genome sequences Completeness assessment of the genome using the Busco tool toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1
8 Braker3 Annotation step with Braker3 toolshed.g2.bx.psu.edu/repos/genouest/braker3/braker3/3.0.8+galaxy2
9 JBrowse instance with the BRAKER3 annotation track JBrowse toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1
10 GFFRead Converts GFF files to other formats, such as FASTA toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.4+galaxy0
11 OMArk OMArk toolshed.g2.bx.psu.edu/repos/iuc/omark/omark/0.3.1+galaxy1
12 BUSCO on the predicted protein sequences Completeness assessment of the genome using the Busco tool toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1

Outputs

ID Name Description Type
BUSCO GFF (Genome) #main/BUSCO GFF (Genome) n/a
  • File
BUSCO GFF (Predicted Proteins) #main/BUSCO GFF (Predicted Proteins) n/a
  • File
BUSCO Missing Genes (Genome) #main/BUSCO Missing Genes (Genome) n/a
  • File
BUSCO Missing Genes (Predicted Proteins) #main/BUSCO Missing Genes (Predicted Proteins) n/a
  • File
BUSCO Summary (Genome) #main/BUSCO Summary (Genome) n/a
  • File
BUSCO Summary (Predicted Proteins) #main/BUSCO Summary (Predicted Proteins) n/a
  • File
BUSCO Summary Image (Genome) #main/BUSCO Summary Image (Genome) n/a
  • File
BUSCO Summary Image (Predicted Proteins) #main/BUSCO Summary Image (Predicted Proteins) n/a
  • File
BUSCO Table (Genome) #main/BUSCO Table (Genome) n/a
  • File
BUSCO Table (Predicted Proteins) #main/BUSCO Table (Predicted Proteins) n/a
  • File
Braker3 Annotation GFF #main/Braker3 Annotation GFF n/a
  • File
JBrowse Genome Browser #main/JBrowse Genome Browser n/a
  • File
OMArk Detailed Summary #main/OMArk Detailed Summary n/a
  • File
OMArk Summary #main/OMArk Summary n/a
  • File
Predicted Proteins #main/Predicted Proteins n/a
  • File

Version History

v0.1 (earliest) Created 9th Dec 2025 at 03:02 by WorkflowHub Bot

Updated to v0.1


Frozen v0.1 3bd4a46
help Creators and Submitter
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License
MIT License (MIT)
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Created: 9th Dec 2025 at 03:01

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