ERGA Annotation
OverviewA collection of workflows designed to annotate elements of the genome. These include repeat regions, protein-coding genes, ncRNA, miRNA.
Space: ERGA
SEEK ID: https://workflowhub.eu/projects/191
Public web page: Not specified
Organisms: No Organisms specified
WorkflowHub PALs: No PALs for this Team
Team created: 7th Sep 2023
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Related items
Teams: ERGA Assembly, ERGA Annotation
Organizations: University of Lausanne
https://orcid.org/0000-0003-4771-6113
Teams: ERGA Assembly, ERGA Annotation
Organizations: Applied Omics Wóycicki
https://orcid.org/0000-0001-7991-7150
Welcome to the ERGA Space!
Here we collect, curate and develop pipelines to assemble and annotation reference-quality genomes for all eukaryotic life.
For Genome Assembly pipelines head to our Assembly Team
For Genome Annotation pipelines head to our Annotation Team
Development, discussions and issue tracking takes place in the ERGA github repo
If you would like to join ...
Teams: ERGA Assembly, ERGA Annotation
Web page: https://www.erga-biodiversity.eu/
Country: 
France
City: Paris
Web page: https://jacob.cea.fr/drf/ifrancoisjacob/Pages/Departements/Genoscope.aspx
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.
ANNOTATO - Annotation workflow To Annotate Them Oll
ERGA Protein-coding gene annotation workflow.
Adapted from the work of Sagane Joye:
https://github.com/sdind/genome_annotation_workflow
Prerequisites
The following programs are required to run the workflow and the listed version were tested. It should be noted that older versions of snakemake are not compatible with newer versions of singularity as is noted here: https://github.com/nextflow-io/nextflow/issues/1659.
conda v 23.7.3
...
