Phred/Phrap/Consed/Polyphred:类Unix平台的测序数据管理和SNP识别软件包

尽管二代基因组测序技术日渐流行,Sanger测序依旧是SNP识别和分析的金标准。传统对于Sanger测序结果的分析多依赖Seq Man等软件进行。然而这类软件大多依靠人工操作来识别和记录测序结果中的SNP位点,效率低下且容易发生错误。此外,当对多个个体进行序列测定时,这类软件无法完成对群体数据的管理和输出,给研究人员造成了一定的不便。Phred/Phrap/Consed/Polyphred是华盛顿大学开发的基于类Unix平台的软件包,在大规模测序数据的管理和SNP自动识别、标记与输出方面具有强大的功能。然而,由于其安装和使用较为复杂,在国内较少使用。本研究对该软件包的功能、使用流程、特点等进行了介绍,并将其安装于Ubuntu12.04操作系统并置于VMware虚拟机中,方便遗传学者的下载和使用。

Phred/Phrap/Consed/Polyphred: a software package for sequencing data management and SNP detection on Unix-like platform

Although next-generation sequencing is more and more popular in current era, Sanger sequencing is still the gold standard for SNP detection and analysis. The analysis for Sanger sequencing is usually performed by softwares such as SeqMan. However, these softwares usually identify and record SNPs manually, which is low-efficiency and prone to error. Moreover, when multiple individuals are involved for sequencing, these softwares cannot organize and output the result for population, which cause some inconvenience for researchers. Phred/Phrap/Consed/Polyphred is a software package based on Unix-like operating system from University of Washington with powerful function in sequencing data manage and SNP detection, mark, and output. However, due to the complexity in setup and utilizing, this package is hardly used in Chinese genetic community. The function, working flow, and character of this package were introduced. Moreover, the software was installed in Ubuntu and enclosed in VMware virtual machine, which can facilitate the download and usage for genetic researchers.