compare_genomes: a comparative genomics workflow to streamline the analysis of evolutionary divergence across genomes

Abstract

SummaryThe 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 often deploy multiple, often purpose-built frameworks, limiting their transferability and replicability. Here, we developed compare_genomes, a transferable and extensible comparative genomics workflow package which streamlines the identification of orthologous families within and across genomes and tests for the presence of several mechanisms of evolution (gene family expansion or contraction and substitution rates within protein-coding sequences). Availability and ImplementationThe workflow is available for Linux, written as a Nextflow workflow which calls established genomics and phylogenetics tools to streamline the analysis and visualisation of genome divergence. This workflow is freely available at https://github.com/jeffersonfparil/compare_genomes, distributed under the GNU General Public License version 3 (GPLv3). ContactCorresponding author: Jeff Paril jeff.paril@unimelb.edu.au. Queries and issues regarding the implementation can be submitted on the issue page of the github repository: https://github.com/jeffersonfparil/compare_genomes/issues. Supplementary informationSynonymous to non-synonymous (Ka/Ks) nucleotide substitution ratio plots for the example data set are found in the github repository.