School of BioSciences, University of Melbourne, Parkville, Victoria, Australia.
Curr Protoc. 2023 Aug;3(8):e876. doi: 10.1002/cpz1.876.
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 https://github.com/jeffersonfparil/compare_genomes, distributed under the GNU General Public License version 3 (GPLv3). © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: Comparative genomics with Nextflow and Conda.
性价比高的基因组组装技术的出现，使得通过比较多个物种的基因组，深入开展比较基因组学研究来解决基本的进化问题成为可能。然而，比较基因组学分析通常会使用多个专门构建的框架，这限制了它们的可转移性和可重复性。在这里，我们介绍了 compare_genomes，这是一个可转移和可扩展的比较基因组学工作流程包，它简化了在真核生物基因组内和跨基因组中鉴定直系同源家族的过程，并测试了几种进化机制（基因家族的扩张或收缩以及蛋白质编码序列中的替换率）的存在。该工作流程适用于 Linux，它被编写为一个 Nextflow 工作流程，调用成熟的基因组学和系统发生学工具，以简化真核生物基因组分化的分析和可视化。该工作流程可在 https://github.com/jeffersonfparil/compare_genomes 免费获取，根据 GNU 通用公共许可证第 3 版（GPLv3）分发。© 2023 作者。当前协议由 Wiley Periodicals LLC 出版。基础方案：使用 Nextflow 和 Conda 进行比较基因组学。
