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	BOAT: Basic Oligonucleotide Alignment Tool
	Zhao, Shu-Qi ; Wang, Jun ; Zhang, Li ; Li, Jiong-Tang ; Gu, Xiaocheng ; Gao, Ge ; Wei, Liping
	2009
关键词	GENOME GENERATION MILLIONS BLAST
英文摘要	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. Conclusion: 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.; Biotechnology & Applied Microbiology; Genetics & Heredity; SCI(E); CPCI-S(ISTP); PubMed; 5
语种	英语
DOI标识	10.1186/1471-2164-10-S3-S2
内容类型	其他
源URL	[http://ir.pku.edu.cn/handle/20.500.11897/162588]
专题	生命科学学院
推荐引用方式 GB/T 7714	Zhao, Shu-Qi,Wang, Jun,Zhang, Li,et al. BOAT: Basic Oligonucleotide Alignment Tool. 2009-01-01.

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