snakePipes: facilitating flexible, scalable and integrative epigenomic analysis
snakePipes: facilitating flexible, scalable and integrative epigenomic analysis
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DOI：
10.1093/bioinformatics/btz436
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发表时间：
2019-11-15
期刊：
影响因子：
5.8
通讯作者：
Manke, Thomas
中科院分区：
文献类型：
--
作者：
Bhardwaj, Vivek;Heyne, Steffen;Manke, Thomas
摘要：由于表观基因组数据的规模和多样性迅速增加，模块化和可扩展的分析工作流程受到广泛关注。在这里，我们介绍了snakePipes，一个用于处理和下游分析常见表观基因组测定数据的工作流程包：ChIP-seq，RNA-seq，Bisulfite-seq，ATAC-seq，Hi-C和单细胞RNA-seq。snakePipes使用户能够组装每个工作流的变体，并通过其简单的命令行包装器和yaml文件轻松安装和升级底层工具。
The Summary: Due to the rapidly increasing scale and diversity of epigenomic data, modular and scalable analysis workflows are of wide interest. Here we present snakePipes, a workflow package for processing and downstream analysis of data from common epigenomic assays: ChIP-seq, RNA-seq, Bisulfite-seq, ATAC-seq, Hi-C and single-cell RNA-seq. snakePipes enables users to assemble variants of each workflow and to easily install and upgrade the underlying tools, via its simple command-line wrappers and yaml files.