Laboratory for Bioinformatics and Computational Genomics, Department of Molecular Biotechnology, Ghent University, 9000 Ghent, Belgium.
BMC Bioinformatics. 2010 May 20;11:269. doi: 10.1186/1471-2105-11-269.
Next-generation amplicon sequencing enables high-throughput genetic diagnostics, sequencing multiple genes in several patients together in one sequencing run. Currently, no open-source out-of-the-box software solution exists that reliably reports detected genetic variations and that can be used to improve future sequencing effectiveness by analyzing the PCR reactions.
We developed an integrated database oriented software pipeline for analysis of 454/Roche GS-FLX amplicon resequencing experiments using Perl and a relational database. The pipeline enables variation detection, variation detection validation, and advanced data analysis, which provides information that can be used to optimize PCR efficiency using traditional means. The modular approach enables customization of the pipeline where needed and allows researchers to adopt their analysis pipeline to their experiments. Clear documentation and training data is available to test and validate the pipeline prior to using it on real sequencing data.
We designed an open-source database oriented pipeline that enables advanced analysis of 454/Roche GS-FLX amplicon resequencing experiments using SQL-statements. This modular database approach allows easy coupling with other pipeline modules such as variant interpretation or a LIMS system. There is also a set of standard reporting scripts available.
下一代扩增子测序能够实现高通量基因诊断，可在一次测序运行中对多个患者的多个基因进行测序。目前，尚无可靠报告检测到的遗传变异的开源即用型软件解决方案，也无法通过分析 PCR 反应来提高未来测序的有效性。
我们使用 Perl 和关系数据库开发了一个用于分析 454/Roche GS-FLX 扩增重测序实验的集成数据库导向软件流水线。该流水线能够进行变异检测、变异检测验证和高级数据分析，提供可用于优化 PCR 效率的信息，采用传统方法。模块化方法可以根据需要定制流水线，并允许研究人员根据自己的实验采用分析流水线。在使用真实测序数据之前，可以使用清晰的文档和培训数据对流水线进行测试和验证。
我们设计了一个开源的数据库导向流水线，能够使用 SQL 语句对 454/Roche GS-FLX 扩增重测序实验进行高级分析。这种模块化的数据库方法允许与其他流水线模块（如变体解释或 LIMS 系统）轻松耦合。还提供了一组标准报告脚本。
