title: ngsCAT: a tool to assess the efficiency of targeted enrichment sequencing.
abstract: BACKGROUND
  Targeted enrichment sequencing by next-generation sequencing is a common approach to interrogate specific loci or the whole exome in the human genome. The efficiency and the lack of bias in the enrichment process need to be assessed as a quality control step before performing downstream analysis of the sequence data. Tools that can report on the sensitivity, specificity, uniformity and other enrichment-specific features are needed.
  
  
  RESULTS
  We have implemented the next-generation sequencing data Capture Assessment Tool (ngsCAT), a tool that takes the information of the mapped reads and the coordinates of the targeted regions as input files, and generates a report with metrics and figures that allows the evaluation of the efficiency of the enrichment process. The tool can also take as input the information of two samples allowing the comparison of two different experiments.
  
  
  METHODS
  Documentation and downloads for ngsCAT can be found at http://www.bioinfomgp.org/ngscat.
authors.affiliation: Bioinformatics Department, Genomics and Bioinformatics Platform of Andalusia (GBPA), 41092 Seville, Computational Genomics Department, Centro de Investigación Príncipe Felipe, 46012 Valencia, Spain and Functional Genomics Node (INB), Centro de Investigación Príncipe Felipe, 46012 Valencia, Spain.
authors.forename: Francisco J
authors.initials: FJ
authors.lastname: López-Domingo
authors.affiliation: Bioinformatics Department, Genomics and Bioinformatics Platform of Andalusia (GBPA), 41092 Seville, Computational Genomics Department, Centro de Investigación Príncipe Felipe, 46012 Valencia, Spain and Functional Genomics Node (INB), Centro de Investigación Príncipe Felipe, 46012 Valencia, Spain.
authors.forename: Javier P
authors.initials: JP
authors.lastname: Florido
authors.affiliation: Bioinformatics Department, Genomics and Bioinformatics Platform of Andalusia (GBPA), 41092 Seville, Computational Genomics Department, Centro de Investigación Príncipe Felipe, 46012 Valencia, Spain and Functional Genomics Node (INB), Centro de Investigación Príncipe Felipe, 46012 Valencia, Spain.
authors.forename: Antonio
authors.initials: A
authors.lastname: Rueda
authors.affiliation: Bioinformatics Department, Genomics and Bioinformatics Platform of Andalusia (GBPA), 41092 Seville, Computational Genomics Department, Centro de Investigación Príncipe Felipe, 46012 Valencia, Spain and Functional Genomics Node (INB), Centro de Investigación Príncipe Felipe, 46012 Valencia, SpainBioinformatics Department, Genomics and Bioinformatics Platform of Andalusia (GBPA), 41092 Seville, Computational Genomics Department, Centro de Investigación Príncipe Felipe, 46012 Valencia, Spain and Functional Genomics Node (INB), Centro de Investigación Príncipe Felipe, 46012 Valencia, SpainBioinformatics Department, Genomics and Bioinformatics Platform of Andalusia (GBPA), 41092 Seville, Computational Genomics Department, Centro de Investigación Príncipe Felipe, 46012 Valencia, Spain and Functional Genomics Node (INB), Centro de Investigación Príncipe Felipe, 46012 Valencia, Spain.
authors.forename: Joaquín
authors.initials: J
authors.lastname: Dopazo
authors.affiliation: Bioinformatics Department, Genomics and Bioinformatics Platform of Andalusia (GBPA), 41092 Seville, Computational Genomics Department, Centro de Investigación Príncipe Felipe, 46012 Valencia, Spain and Functional Genomics Node (INB), Centro de Investigación Príncipe Felipe, 46012 Valencia, Spain.
authors.forename: Javier
authors.initials: J
authors.lastname: Santoyo-Lopez
mesh_terms: D059472:Exome; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software