title: NextGenMap: fast and accurate read mapping in highly polymorphic genomes.
abstract: CONCLUSIONS
  When choosing a read mapper, one faces the trade off between speed and the ability to map reads in highly polymorphic regions. Here, we report NextGenMap, a fast and accurate read mapper, which reduces this dilemma. NextGenMap aligns reads reliably to a reference genome even when the sequence difference between target and reference genome is large, i.e. highly polymorphic genome. At the same time, NextGenMap outperforms current mapping methods with respect to runtime and to the number of correctly mapped reads. NextGenMap efficiently uses the available hardware by exploiting multi-core CPUs as well as graphic cards (GPUs), if available. In addition, NextGenMap handles automatically any read data independent of read length and sequencing technology.
  
  
  BACKGROUND
  NextGenMap source code and documentation are available at: http://cibiv.github.io/NextGenMap/.
  
  
  BACKGROUND
  fritz.sedlazeck@univie.ac.at.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors: Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria and Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Waehringerstrasse 17, A-1090 Vienna, Austria.
authors: Fritz J
authors: FJ
authors: Sedlazeck
authors: Philipp
authors: P
authors: Rescheneder
authors: Arndt
authors: A
authors: von Haeseler
mesh_terms: D016678:Genome; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D011110:Polymorphism, Genetic; D016415:Sequence Alignment / Q000379:methods*; D012984:Software