ERGA-BGE Genome Report ANNOT analyses

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Workflow Type: Galaxy
Stable

The workflow requires the user to provide:

  • ENSEMBL link address of the annotation GFF3 file
  • ENSEMBL link address of the assembly FASTA file
  • NCBI taxonomy ID
  • BUSCO lineage
  • OMArk database

Thw workflow will produce statistics of the annotation based on AGAT, BUSCO and OMArk.

SEEK ID: https://workflowhub.eu/workflows/1096?version=2

Inputs

ID Name Description Type
BUSCO Lineage BUSCO Lineage Choose the (eukaryotic) BUSCO lineage that corresponds to the assembled species. EXAMPLE: mammalia_odb10
  • string
Enter GFF3 ENSEMBL link Enter GFF3 ENSEMBL link EXAMPLE: https://ftp.ebi.ac.uk/pub/ensemblorganisms/Arca_noae/GCA_964261245.1/ensembl/geneset/2024_11/genes.gff3 OR https://ftp.ensembl.org/pub/rapid-release/species/Apodemus_agrarius/GCA_964023405.1/ensembl/geneset/2024_05/Apodemus_agrarius-GCA_964023405.1-2024_05-genes.gff3.gz
  • string
Enter NCBI taxonomy ID Enter NCBI taxonomy ID EXAMPLE: 39030 (Can be obtained from: https://www.ncbi.nlm.nih.gov/taxonomy)
  • string
Enter genome ENSEMBL link Enter genome ENSEMBL link EXAMPLE: https://ftp.ebi.ac.uk/pub/ensemblorganisms/Arca_noae/GCA_964261245.1/genome/unmasked.fa.gz OR https://ftp.ensembl.org/pub/rapid-release/species/Apodemus_agrarius/GCA_964023405.1/ensembl/genome/Apodemus_agrarius-GCA_964023405.1-unmasked.fa.gz
  • string
Is the GFF compressed? (gff3.gz) Is the GFF compressed? (gff3.gz) n/a
  • boolean
Select OMArk database Select OMArk database n/a
  • string

Steps

ID Name Description
6 Create text file toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1
7 Create text file toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1
8 downloads lftp
9 downloads lftp
10 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
11 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
12 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
13 Pick parameter value toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
14 AGAT toolshed.g2.bx.psu.edu/repos/bgruening/agat/agat/1.2.0+galaxy1
15 AGAT toolshed.g2.bx.psu.edu/repos/bgruening/agat/agat/1.2.0+galaxy2
16 AGAT toolshed.g2.bx.psu.edu/repos/bgruening/agat/agat/1.2.0+galaxy1
17 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0
18 OMArk toolshed.g2.bx.psu.edu/repos/iuc/omark/omark/0.3.0+galaxy2

Version History

Version 2 (latest) Created 5th Feb 2025 at 21:21 by Diego De Panis

No revision comments

Frozen Version-2 35eb999

Version 1 (earliest) Created 9th Aug 2024 at 15:14 by Diego De Panis

Initial commit


Frozen Version-1 c0ef3ff
help Creators and Submitter
Creator
Additional credit

ERGA

Submitter
Discussion Channel
https://github.com/ERGA-consortium/pipelines/discussions
Tools
AGAT
BUSCO
OMArk
License
MIT License
Activity

Views: 1828   Downloads: 266   Runs: 27

Created: 9th Aug 2024 at 15:14

Last updated: 24th Feb 2025 at 15:24

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