Compare_Genomes: A Comparative Genomics Workflow to Streamline the Analysis of Evolutionary Divergence Across Eukaryotic Genomes
Jefferson Paril, Tannaz Zare, Alexandre Fournier‐Level- Medical Laboratory Technology
- Health Informatics
- General Pharmacology, Toxicology and Pharmaceutics
- General Immunology and Microbiology
- General Biochemistry, Genetics and Molecular Biology
- General Neuroscience
Abstract
The dawn of cost‐effective genome assembly is enabling deep comparative genomics to address fundamental evolutionary questions by comparing the genomes of multiple species. However, comparative genomics analyses frequently deploy multiple, often purpose‐built frameworks, limiting their transferability and replicability. Here, we present compare_genomes, a transferable and extensible comparative genomics workflow package we developed that streamlines the identification of orthologous families within and across eukaryotic genomes and tests for the presence of several mechanisms of evolution (gene family expansion or contraction and substitution rates within protein‐coding sequences). The workflow is available for Linux, written as a Nextflow workflow that calls established genomics and phylogenetics tools to streamline the analysis and visualization of eukaryotic genome divergence. This workflow is freely available at
Basic Protocol: Comparative genomics with Nextflow and Conda