title: HSA: a heuristic splice alignment tool.
abstract: BACKGROUND
  RNA-Seq methodology is a revolutionary transcriptomics sequencing technology, which is the representative of Next generation Sequencing (NGS). With the high throughput sequencing of RNA-Seq, we can acquire much more information like differential expression and novel splice variants from deep sequence analysis and data mining. But the short read length brings a great challenge to alignment, especially when the reads span two or more exons.
  
  
  METHODS
  A two steps heuristic splice alignment tool is generated in this investigation. First, map raw reads to reference with unspliced aligner--BWA; second, split initial unmapped reads into three equal short reads (seeds), align each seed to the reference, filter hits, search possible split position of read and extend hits to a complete match.
  
  
  RESULTS
  Compare with other splice alignment tools like SOAPsplice and Tophat2, HSA has a better performance in call rate and efficiency, but its results do not as accurate as the other software to some extent.
  
  
  CONCLUSIONS
  HSA is an effective spliced aligner of RNA-Seq reads mapping, which is available at https://github.com/vlcc/HSA.
authors.forename: Jingde
authors.initials: J
authors.lastname: Bu
authors.forename: Xuebin
authors.initials: X
authors.lastname: Chi
authors.forename: Zhong
authors.initials: Z
authors.lastname: Jin
mesh_terms: D019295:Computational Biology / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D011381:Programming Languages; D012326:RNA Splicing; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA; D013997:Time Factors