Eco-Flow/excon

Eco-Flow/excon is a Nextflow pipeline -written using the nf-core standards- that runs gene family expansion and contraction analysis (via CAFE). This pipeline automates the analysis to run the basic steps in EXpansion and CONtraction of gene families, as well as running GO enrichment analysis on the output.

Overview

Roughly, the pipeline performs the following steps:

• Describes the genome assembly and annotation: completness, contiguity and general gene stats (e.g., number of genes, exons, introns).
• Identifies orthologous genes across assemblies.
• Detects gene family expansion and contraction based on orthologous gene groups.
• Performs Gene Ontology annotation on orthologous genes.

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