Eco-Flow/synteny

Eco-Flow/synteny is a Nextflow pipeline -written using the nf-core standards- for comparing gene synteny between chromosome level genome assemblies. It takes genomes and annotations files as inputs and assesses macrosynteny using a suit of tools.

Overview

At a high level, the workflow performs the following steps:

• Downloads chromosome-level genome assemblies and annotations.
• Identifies orthologous genes across species.
• Detects syntenyc blocks and structural rearrangements.
• Produces synteny visualizations and summary tables.

For additional details, usage instructions, and examples, please refer to the Eco-Flow/synteny GitHub repository.