Software for the analysis of large-scale genotyping and sequencing studies

这个项目的目标是开发软件来分析来自大型- 在现有软件的基础上进行大规模的基因分型和基因测序研究 包裹叮当作响。操纵和分析全基因组SNP的软件工具Plink 在过去四年中积极开发并具有广泛基础的数据集 用户的数量。具体目标是显著提升核心能力、接口、 辅助资源和用户支助：核心能力：显著调整和升级 数据存储容量，可处理的数据集比可容纳的数据集大一个数量级 记忆和b)不同类型基因的更一般、统一的表示 变异数据和元信息。接口：扩展现有接口以提供) 通过多个接口实现数据存储和分析组件之间的松散耦合 外部语言，包括标准生物信息学工具，如R和Perl，以及b) 旨在促进可重复性研究和并行处理的功能。辅机 资源：打包标准的现有资源，包括 变异、参考基因组序列和基因组合、途径和本体论， 以允许基因组资源和用户数据之间无缝集成的方式。 支持：创建高质量的馆藏资源，支持用户，通过线上 文档和教程，包括用户生成的维基页面、电子邮件支持和 一年一度的培训课程。将特别注意确保与 其他主要软件、文件格式和更广泛的 遗传学社区。

The objective of this project is to develop software for the analysis of data from large- scale genotyping and sequencing genetic studies, building on the existing software package PLINK. PLINK, a software tool to manipulate and analyze whole-genome SNP datasets that has been actively developed over the past four years and has a wide base of users. The specific aims are to significantly upgrade core capacities, the interface, auxiliary resources and user-support: Core capacities: significantly adapt and upgrade data-storage capacities to handle a) order-of-magnitude larger datasets than can fit into memory and b) a more generic, unified representation of different types of genetic variation data and meta-information. Interface: extend the existing interface to provide a) a looser coupling between data storage and analysis components, via multiple interfaces in external languages, including standard bioinformatics tools such as R and Perl, and b) features designed to facilitate reproducible research and parallel processing. Auxiliary resources: package standard existing resources, including the functional annotation of variants, reference genome sequences and gene assemblies, pathways and ontologies, in a manner that allows seamless integration between genomic resources and user data. Support: create a high-quality collection resources to support users, via online documentation and tutorials, including user-generated wiki pages, e-mail support and an annual training course. Particular attention will be paid to ensure interoperability with other major software, file-formats and resources that are generated by the broader genetics community.