title: Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data.
abstract: BACKGROUND
  Detection of random errors and systematic biases is a crucial step of a robust pipeline for processing high-throughput sequencing (HTS) data. Bioinformatics software tools capable of performing this task are available, either for general analysis of HTS data or targeted to a specific sequencing technology. However, most of the existing QC instruments only allow processing of one sample at a time.
  
  
  RESULTS
  Qualimap 2 represents a next step in the QC analysis of HTS data. Along with comprehensive single-sample analysis of alignment data, it includes new modes that allow simultaneous processing and comparison of multiple samples. As with the first version, the new features are available via both graphical and command line interface. Additionally, it includes a large number of improvements proposed by the user community.
  
  
  METHODS
  The implementation of the software along with documentation is freely available at http://www.qualimap.org.
  
  
  BACKGROUND
  meyer@mpiib-berlin.mpg.de
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Molecular Biology, Max Planck Institute for Infection Biology, D-10117, Berlin, Germany.
authors.forename: Konstantin
authors.initials: K
authors.lastname: Okonechnikov
authors.affiliation: Genomics of Gene Expression Lab, Centro de Investigación Príncipe Felipe, 46012, Valencia, Spain and Microbiology and Cell Science Department, Institute for Food and Agricultural Research, University of Florida at Gainesville, FL 32611-0700, USA.
authors.forename: Ana
authors.initials: A
authors.lastname: Conesa
authors.affiliation: Department of Molecular Biology, Max Planck Institute for Infection Biology, D-10117, Berlin, Germany.
authors.forename: Fernando
authors.initials: F
authors.lastname: García-Alcalde
mesh_terms: D000465:Algorithms; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D011786:Quality Control; D016415:Sequence Alignment / Q000592:standards*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software