title: GBSX: a toolkit for experimental design and demultiplexing genotyping by sequencing experiments.
abstract: BACKGROUND
  Massive parallel sequencing is a powerful tool for variant discovery and genotyping. To reduce costs, sequencing of restriction enzyme based reduced representation libraries can be utilized. This technology is generally referred to as Genotyping By Sequencing (GBS). To deal with GBS experimental design and initial processing specific bioinformatic tools are needed.
  
  
  RESULTS
  GBSX is a package that assists in selecting the appropriate enzyme and the design of compatible in-line barcodes. Post sequencing, it performs optimized demultiplexing using these barcodes to create fastq files per barcode which can easily be plugged into existing variant analysis pipelines. Here we demonstrate the usability of the GBSX toolkit and demonstrate improved in-line barcode demultiplexing and trimming performance compared to existing tools.
  
  
  CONCLUSIONS
  GBSX provides an easy to use suite of tools for designing and demultiplexing of GBS experiments.
authors.affiliation: Center for Human Genetics, KU Leuven, Herestraat 49, Leuven, 3000, Belgium. koen.herten@med.kuleuven.be.|Genomics Core, UZ Leuven, Herestraat 49, Leuven, 3000, Belgium. koen.herten@med.kuleuven.be.
authors.forename: Koen
authors.initials: K
authors.lastname: Herten
authors.affiliation: Center for Human Genetics, KU Leuven, Herestraat 49, Leuven, 3000, Belgium. matthew.hestand@med.kuleuven.be.
authors.forename: Matthew S
authors.initials: MS
authors.lastname: Hestand
authors.affiliation: Center for Human Genetics, KU Leuven, Herestraat 49, Leuven, 3000, Belgium. joris.vermeesch@med.kuleuven.be.|Genomics Core, UZ Leuven, Herestraat 49, Leuven, 3000, Belgium. joris.vermeesch@med.kuleuven.be.
authors.forename: Joris R
authors.initials: JR
authors.lastname: Vermeesch
authors.affiliation: Center for Human Genetics, KU Leuven, Herestraat 49, Leuven, 3000, Belgium. jeroen.vanhoudt@med.kuleuven.be.|Genomics Core, UZ Leuven, Herestraat 49, Leuven, 3000, Belgium. jeroen.vanhoudt@med.kuleuven.be.
authors.forename: Jeroen K J
authors.initials: JK
authors.lastname: Van Houdt
mesh_terms: D004262:DNA Restriction Enzymes; D060005:Genotyping Techniques / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D004262:DNA Restriction Enzymes