Technical University of Munich, Institute for Advanced Study (IAS), Lichtenbergstr. 2a, Garching, 85748, Germany.
Technical University of Munich, Department of Plant Sciences, Liesel-Beckmann-Str. 2, Freising, 85354, Germany.
BMC Genomics. 2020 Jul 13;21(1):479. doi: 10.1186/s12864-020-06886-3.
Whole-Genome Bisulfite Sequencing (WGBS) is a Next Generation Sequencing (NGS) technique for measuring DNA methylation at base resolution. Continuing drops in sequencing costs are beginning to enable high-throughput surveys of DNA methylation in large samples of individuals and/or single cells. These surveys can easily generate hundreds or even thousands of WGBS datasets in a single study. The efficient pre-processing of these large amounts of data poses major computational challenges and creates unnecessary bottlenecks for downstream analysis and biological interpretation.
To offer an efficient analysis solution, we present MethylStar, a fast, stable and flexible pre-processing pipeline for WGBS data. MethylStar integrates well-established tools for read trimming, alignment and methylation state calling in a highly parallelized environment, manages computational resources and performs automatic error detection. MethylStar offers easy installation through a dockerized container with all preloaded dependencies and also features a user-friendly interface designed for experts/non-experts. Application of MethylStar to WGBS from Human, Maize and A. thaliana shows favorable performance in terms of speed and memory requirements compared with existing pipelines.
MethylStar is a fast, stable and flexible pipeline for high-throughput pre-processing of bulk or single-cell WGBS data. Its easy installation and user-friendly interface should make it a useful resource for the wider epigenomics community. MethylStar is distributed under GPL-3.0 license and source code is publicly available for download from github https://github.com/jlab-code/MethylStar . Installation through a docker image is available from http://jlabdata.org/methylstar.tar.gz.
全基因组亚硫酸氢盐测序（WGBS）是一种用于以碱基分辨率测量 DNA 甲基化的下一代测序（NGS）技术。测序成本的持续下降开始使对个体和/或单细胞的大量样本中的 DNA 甲基化进行高通量调查成为可能。这些调查在单个研究中很容易生成数百甚至数千个 WGBS 数据集。这些大量数据的有效预处理给计算带来了重大挑战，并为下游分析和生物学解释造成了不必要的瓶颈。
为了提供有效的分析解决方案，我们提出了 MethylStar，这是一种用于 WGBS 数据的快速、稳定和灵活的预处理流水线。MethylStar 集成了经过验证的工具，用于在高度并行化的环境中进行读取修剪、比对和甲基化状态调用，管理计算资源并执行自动错误检测。MethylStar 通过带有所有预加载依赖项的 docker 容器进行轻松安装，并且具有为专家/非专家设计的用户友好界面。MethylStar 在人类、玉米和拟南芥的 WGBS 中的应用在速度和内存需求方面表现出优于现有管道的良好性能。
MethylStar 是一种用于批量或单细胞 WGBS 数据的高通量预处理的快速、稳定和灵活的流水线。其简单的安装和用户友好的界面应该使其成为更广泛的表观基因组学社区的有用资源。MethylStar 是在 GPL-3.0 许可证下分发的，源代码可从 github https://github.com/jlab-code/MethylStar 下载。通过 docker 映像进行安装可从 http://jlabdata.org/methylstar.tar.gz 获得。
