Analysing 454 amplicon resequencing experiments using the modular and database oriented Variant Identification Pipeline.
作者： Joachim M De Schrijver , Kim De Leeneer , Steve Lefever , Nick Sabbe , Filip Pattyn
关键词: Set (abstract data type) 、 Pipeline (software) 、 Biology 、 Software 、 Database 、 Identification (information) 、 Modular design 、 Perl 、 Relational database 、 Amplicon
摘要: Next-generation amplicon sequencing enables high-throughput genetic diagnostics, multiple genes in several patients together one run. Currently, no open-source out-of-the-box software solution exists that reliably reports detected variations and can be used to improve future effectiveness by analyzing the PCR reactions. We developed an integrated database oriented pipeline for analysis of 454/Roche GS-FLX resequencing experiments using Perl a relational database. The variation detection, detection validation, advanced data analysis, which provides information optimize efficiency traditional means. modular approach customization where needed allows researchers adopt their experiments. Clear documentation training is available test validate prior it on real data. designed SQL-statements. This easy coupling with other modules such as variant interpretation or LIMS system. There also set standard reporting scripts available.
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