title: BOAT: Basic Oligonucleotide Alignment Tool.
abstract: BACKGROUND
  Next-generation DNA sequencing technologies generate tens of millions of sequencing reads in one run. These technologies are now widely used in biology research such as in genome-wide identification of polymorphisms, transcription factor binding sites, methylation states, and transcript expression profiles. Mapping the sequencing reads to reference genomes efficiently and effectively is one of the most critical analysis tasks. Although several tools have been developed, their performance suffers when both multiple substitutions and insertions/deletions (indels) occur together.
  
  
  RESULTS
  We report a new algorithm, Basic Oligonucleotide Alignment Tool (BOAT) that can accurately and efficiently map sequencing reads back to the reference genome. BOAT can handle several substitutions and indels simultaneously, a useful feature for identifying SNPs and other genomic structural variations in functional genomic studies. For better handling of low-quality reads, BOAT supports a "3'-end Trimming Mode" to build local optimized alignment for sequencing reads, further improving sensitivity. BOAT calculates an E-value for each hit as a quality assessment and provides customizable post-mapping filters for further mapping quality control.
  
  
  CONCLUSIONS
  Evaluations on both real and simulation datasets suggest that BOAT is capable of mapping large volumes of short reads to reference sequences with better sensitivity and lower memory requirement than other currently existing algorithms. The source code and pre-compiled binary packages of BOAT are publicly available for download at http://boat.cbi.pku.edu.cn under GNU Public License (GPL). BOAT can be a useful new tool for functional genomics studies.
authors: Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, PR China. zhaosq@mail.cbi.pku.edu.cn
authors: Shu-Qi
authors: SQ
authors: Zhao
authors: Jun
authors: J
authors: Wang
authors: Li
authors: L
authors: Zhang
authors: Jiong-Tang
authors: JT
authors: Li
authors: Xiaocheng
authors: X
authors: Gu
authors: Ge
authors: G
authors: Gao
authors: Liping
authors: L
authors: Wei
mesh_terms: D000465:Algorithms; D023281:Genomics / Q000379:methods*; D006801:Humans; D009841:Oligonucleotides / Q000032:analysis; D020641:Polymorphism, Single Nucleotide; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D009841:Oligonucleotides