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

• ANNOTATO - Annotation workflow To Annotate Them Oll
• Overview of the workflow
• Input data
• Pipeline steps
• Output data
• Prerequisites
• Installation
• Running ANNOTATO
• Before running the pipeline (IMPORTANT) ...

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 ...