title: Fast and accurate long-read alignment with Burrows-Wheeler transform.
abstract: BACKGROUND
  Many programs for aligning short sequencing reads to a reference genome have been developed in the last 2 years. Most of them are very efficient for short reads but inefficient or not applicable for reads >200 bp because the algorithms are heavily and specifically tuned for short queries with low sequencing error rate. However, some sequencing platforms already produce longer reads and others are expected to become available soon. For longer reads, hashing-based software such as BLAT and SSAHA2 remain the only choices. Nonetheless, these methods are substantially slower than short-read aligners in terms of aligned bases per unit time.
  
  
  RESULTS
  We designed and implemented a new algorithm, Burrows-Wheeler Aligner's Smith-Waterman Alignment (BWA-SW), to align long sequences up to 1 Mb against a large sequence database (e.g. the human genome) with a few gigabytes of memory. The algorithm is as accurate as SSAHA2, more accurate than BLAT, and is several to tens of times faster than both.
  
  
  BACKGROUND
  http://bio-bwa.sourceforge.net
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK.
authors.forename: Heng
authors.initials: H
authors.lastname: Li
authors.forename: Richard
authors.initials: R
authors.lastname: Durbin
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D006801:Humans; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA