annotation-maker/main
v0.1

Workflow Type: Galaxy

This workflow allows for genome annotation using Maker and evaluates the quality of the annotation.

Inputs

ID Name Description Type
Augustus training Augustus training Augustus training
  • File
BUSCO lineage BUSCO lineage BUSCO lineage
  • string
Genome assembly Genome assembly Genome assembly
  • File
Genome sequence Genome sequence Genome sequence
  • File
Protein sequences Protein sequences Protein sequences
  • File
SNAP training SNAP training SNAP training
  • File

Steps

ID Name Description
6 Fasta Statistics Fasta Statistics on the genome toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0
7 BUSCO on the genome sequences Completeness assessment of the genome using the Busco tool toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0
8 Maker Annotation with Maker toolshed.g2.bx.psu.edu/repos/iuc/maker/maker/2.31.11+galaxy2
9 GFFRead toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.4+galaxy0
10 Genome annotation statistics Genome annotation statistics on the maker's annotation toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4
11 Map annotation ids toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.11
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/5.7.1+galaxy0
13 JBrowse toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1

Outputs

ID Name Description Type
fasta stats genome fasta stats genome n/a
  • File
busco image genome busco image genome n/a
  • File
busco sum genome busco sum genome n/a
  • File
busco table genome busco table genome n/a
  • File
busco gff genome busco gff genome n/a
  • File
busco missing genome busco missing genome n/a
  • File
maker full maker full n/a
  • File
maker gff maker gff n/a
  • File
maker evidences maker evidences n/a
  • File
gffread exons gffread exons n/a
  • File
graphs genome graphs genome n/a
  • File
summary genome summary genome n/a
  • File
renamed gff3 renamed gff3 n/a
  • File
id map id map n/a
  • File
busco missing predicted proteins busco missing predicted proteins n/a
  • File
busco table predicted proteins busco table predicted proteins n/a
  • File
busco gff predicted proteins busco gff predicted proteins n/a
  • File
busco sum predicted proteins busco sum predicted proteins n/a
  • File
busco image predicted proteins busco image predicted proteins n/a
  • File
jbrowse jbrowse n/a
  • File

Version History

v0.1 (earliest) Created 26th Mar 2025 at 09:50 by WorkflowHub Bot

Updated to v0.1


Frozen v0.1 09ce1ab
help Creators and Submitter
Creator
  • Romane Libouban
Submitter
License
Activity

Views: 31   Downloads: 2   Runs: 0

Created: 26th Mar 2025 at 09:50

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