analysing 454 amplicon resequencing experiments using the modular and database oriented variant identification pipeline分析454年扩增子测序实验识别管道使用模块化和面向数据库的变体.pdfVIP

De Schrijver et al. BMC Bioinformatics 2010, 11:269 /1471-2105/11/269 S O F T W A R E Open Access Software Analysing 454 amplicon resequencing experiments using the modular and database oriented Variant Identification Pipeline 1 2 2 3 2 4,5 Joachim M De Schrijver* , Kim De Leeneer , Steve Lefever , Nick Sabbe , Filip Pattyn , Filip Van Nieuwerburgh , Paul Coucke2,5, Dieter Deforce4,5, Jo Vandesompele2,5, Sofie Bekaert1,5, Jan Hellemans2,5 and Wim Van Criekinge 1,5 Abstract Background: 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. Results: 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. Conclusions: We designed an open-source database oriented pipeline that enables advanced analysis of 454/Roche GS-FLX amplicon resequencing experiments using SQL-statements.