Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA.
Department of Global Ecology, Carnegie Institution for Science, Stanford, CA 94305, USA.
Bioinformatics. 2022 Oct 14;38(20):4809-4811. doi: 10.1093/bioinformatics/btac600.
We developed grenepipe, an all-in-one Snakemake workflow to streamline the data processing from raw high-throughput sequencing data of individuals or populations to genotype variant calls. Our pipeline offers a range of popular software tools within a single configuration file, automatically installs software dependencies, is highly optimized for scalability in cluster environments and runs with a single command.
grenepipe is published under the GPLv3 and freely available at github.com/moiexpositoalonsolab/grenepipe.
我们开发了 grenepipe，这是一个一体化的 Snakemake 工作流程，用于简化从个体或群体的原始高通量测序数据到基因型变异呼叫的数据处理。我们的管道在单个配置文件中提供了一系列流行的软件工具，自动安装软件依赖项，针对集群环境中的可扩展性进行了高度优化，并可以使用单个命令运行。
grenepipe 根据 GPLv3 发布，可在 github.com/moiexpositoalonsolab/grenepipe 上免费获得。
