title: Sensitive and fast mapping of di-base encoded reads.
abstract: BACKGROUND
  Discovering variation among high-throughput sequenced genomes relies on efficient and effective mapping of sequence reads. The speed, sensitivity and accuracy of read mapping are crucial to determining the full spectrum of single nucleotide variants (SNVs) as well as structural variants (SVs) in the donor genomes analyzed.
  
  
  RESULTS
  We present drFAST, a read mapper designed for di-base encoded 'color-space' sequences generated with the AB SOLiD platform. drFAST is specially designed for better delineation of structural variants, including segmental duplications, and is able to return all possible map locations and underlying sequence variation of short reads within a user-specified distance threshold. We show that drFAST is more sensitive in comparison to all commonly used aligners such as Bowtie, BFAST and SHRiMP. drFAST is also faster than both BFAST and SHRiMP and achieves a mapping speed comparable to Bowtie.
  
  
  BACKGROUND
  The source code for drFAST is available at http://drfast.sourceforge.net
authors.affiliation: Department of Genome Sciences, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195-5065, USA.
authors.forename: Farhad
authors.initials: F
authors.lastname: Hormozdiari
authors.forename: Faraz
authors.initials: F
authors.lastname: Hach
authors.forename: S Cenk
authors.initials: SC
authors.lastname: Sahinalp
authors.forename: Evan E
authors.initials: EE
authors.lastname: Eichler
authors.forename: Can
authors.initials: C
authors.lastname: Alkan
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping; D002878:Chromosomes, Human, Pair 1; D014644:Genetic Variation; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D009711:Nucleotides; D020641:Polymorphism, Single Nucleotide; D012984:Software
chemical_list: D009711:Nucleotides