title: SAMBLASTER: fast duplicate marking and structural variant read extraction.
abstract: BACKGROUND
  Illumina DNA sequencing is now the predominant source of raw genomic data, and data volumes are growing rapidly. Bioinformatic analysis pipelines are having trouble keeping pace. A common bottleneck in such pipelines is the requirement to read, write, sort and compress large BAM files multiple times.
  
  
  RESULTS
  We present SAMBLASTER, a tool that reduces the number of times such costly operations are performed. SAMBLASTER is designed to mark duplicates in read-sorted SAM files as a piped post-pass on DNA aligner output before it is compressed to BAM. In addition, it can simultaneously output into separate files the discordant read-pairs and/or split-read mappings used for structural variant calling. As an alignment post-pass, its own runtime overhead is negligible, while dramatically reducing overall pipeline complexity and runtime. As a stand-alone duplicate marking tool, it performs significantly better than PICARD or SAMBAMBA in terms of both speed and memory usage, while achieving nearly identical results.
  
  
  METHODS
  SAMBLASTER is open-source C+ + code and freely available for download from https://github.com/GregoryFaust/samblaster.
authors.affiliation: Department of Biochemistry and Molecular Genetics and Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA.
authors.forename: Gregory G
authors.initials: GG
authors.lastname: Faust
authors.affiliation: Department of Biochemistry and Molecular Genetics and Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA Department of Biochemistry and Molecular Genetics and Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA.
authors.forename: Ira M
authors.initials: IM
authors.lastname: Hall
mesh_terms: D056914:Genomic Structural Variation; D023281:Genomics / Q000379:methods; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software