title: STAR: ultrafast universal RNA-seq aligner.
abstract: BACKGROUND
  Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases.
  
  
  RESULTS
  To align our large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, we experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy.
  
  
  METHODS
  STAR is implemented as a standalone C++ code. STAR is free open source software distributed under GPLv3 license and can be downloaded from http://code.google.com/p/rna-star/.
authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA. dobin@cshl.edu
authors.forename: Alexander
authors.initials: A
authors.lastname: Dobin
authors.forename: Carrie A
authors.initials: CA
authors.lastname: Davis
authors.forename: Felix
authors.initials: F
authors.lastname: Schlesinger
authors.forename: Jorg
authors.initials: J
authors.lastname: Drenkow
authors.forename: Chris
authors.initials: C
authors.lastname: Zaleski
authors.forename: Sonali
authors.initials: S
authors.lastname: Jha
authors.forename: Philippe
authors.initials: P
authors.lastname: Batut
authors.forename: Mark
authors.initials: M
authors.lastname: Chaisson
authors.forename: Thomas R
authors.initials: TR
authors.lastname: Gingeras
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D020869:Gene Expression Profiling; D015894:Genome, Human; D006801:Humans; D012326:RNA Splicing; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods; D012984:Software