title: Analysing 454 amplicon resequencing experiments using the modular and database oriented Variant Identification Pipeline.
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. 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.
authors.affiliation: Laboratory for Bioinformatics and Computational Genomics, Department of Molecular Biotechnology, Ghent University, 9000 Ghent, Belgium. Joachim.DeSchrijver@ugent.be
authors.forename: Joachim M
authors.initials: JM
authors.lastname: De Schrijver
authors.forename: Kim
authors.initials: K
authors.lastname: De Leeneer
authors.forename: Steve
authors.initials: S
authors.lastname: Lefever
authors.forename: Nick
authors.initials: N
authors.lastname: Sabbe
authors.forename: Filip
authors.initials: F
authors.lastname: Pattyn
authors.forename: Filip
authors.initials: F
authors.lastname: Van Nieuwerburgh
authors.forename: Paul
authors.initials: P
authors.lastname: Coucke
authors.forename: Dieter
authors.initials: D
authors.lastname: Deforce
authors.forename: Jo
authors.initials: J
authors.lastname: Vandesompele
authors.forename: Sofie
authors.initials: S
authors.lastname: Bekaert
authors.forename: Jan
authors.initials: J
authors.lastname: Hellemans
authors.forename: Wim
authors.initials: W
authors.lastname: Van Criekinge
mesh_terms: D001483:Base Sequence; D030541:Databases, Genetic; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction / Q000379:methods*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface