title: Gustaf: Detecting and correctly classifying SVs in the NGS twilight zone.
abstract: BACKGROUND
  The landscape of structural variation (SV) including complex duplication and translocation patterns is far from resolved. SV detection tools usually exhibit low agreement, are often geared toward certain types or size ranges of variation and struggle to correctly classify the type and exact size of SVs.
  
  
  RESULTS
  We present Gustaf (Generic mUlti-SpliT Alignment Finder), a sound generic multi-split SV detection tool that detects and classifies deletions, inversions, dispersed duplications and translocations of ≥ 30 bp. Our approach is based on a generic multi-split alignment strategy that can identify SV breakpoints with base pair resolution. We show that Gustaf correctly identifies SVs, especially in the range from 30 to 100 bp, which we call the next-generation sequencing (NGS) twilight zone of SVs, as well as larger SVs >500 bp. Gustaf performs better than similar tools in our benchmark and is furthermore able to correctly identify size and location of dispersed duplications and translocations, which otherwise might be wrongly classified, for example, as large deletions.
authors.affiliation: Department of Computer Science, Freie Universität Berlin, 14195 Berlin, Germany, Research Group Bioinformatics (NG4), Robert Koch Institute, 13353 Berlin, Germany and New York Genome Center, New York, NY 10013, USA Department of Computer Science, Freie Universität Berlin, 14195 Berlin, Germany, Research Group Bioinformatics (NG4), Robert Koch Institute, 13353 Berlin, Germany and New York Genome Center, New York, NY 10013, USA.
authors.forename: Kathrin
authors.initials: K
authors.lastname: Trappe
authors.affiliation: Department of Computer Science, Freie Universität Berlin, 14195 Berlin, Germany, Research Group Bioinformatics (NG4), Robert Koch Institute, 13353 Berlin, Germany and New York Genome Center, New York, NY 10013, USA.
authors.forename: Anne-Katrin
authors.initials: AK
authors.lastname: Emde
authors.affiliation: Department of Computer Science, Freie Universität Berlin, 14195 Berlin, Germany, Research Group Bioinformatics (NG4), Robert Koch Institute, 13353 Berlin, Germany and New York Genome Center, New York, NY 10013, USA.
authors.forename: Hans-Christian
authors.initials: HC
authors.lastname: Ehrlich
authors.affiliation: Department of Computer Science, Freie Universität Berlin, 14195 Berlin, Germany, Research Group Bioinformatics (NG4), Robert Koch Institute, 13353 Berlin, Germany and New York Genome Center, New York, NY 10013, USA.
authors.forename: Knut
authors.initials: K
authors.lastname: Reinert
mesh_terms: D056914:Genomic Structural Variation; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D017384:Sequence Deletion; D012984:Software; D014178:Translocation, Genetic