Sensitive and fast mapping of di-base encoded reads
Sensitive and fast mapping of di-base encoded reads
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DOI：
10.1093/bioinformatics/btr303
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发表时间：
2011-07-15
期刊：
影响因子：
5.8
通讯作者：
Alkan, Can
中科院分区：
文献类型：
--
作者：
Hormozdiari, Farhad;Hach, Faraz;Alkan, Can
动机：发现高通量测序基因组之间的变异依赖于序列读数的高效和有效的映射。读段映射的速度、灵敏度和准确性对于确定所分析的供体基因组中单核苷酸变体（SNV）和结构变体（SV）的完整谱至关重要。结果：我们介绍了drFAST，这是一种读段映射器，专为双碱基编码的“颜色空间”设计AB SOLiD平台生成的序列。drFAST专门设计用于更好地描绘结构变体，包括片段重复，并且能够在用户指定的距离阈值内返回所有可能的图谱位置和短读段的潜在序列变异。我们发现drFAST比所有常用的校准器（如Bowtie、BFAST和SHRiMP）更敏感。drFAST也比BFAST和SHRiMP都快，并且实现了与Bowtie相当的映射速度。
Motivation: Discovering variation among high-throughput sequenced genomes relies on efficient and effective mapping of sequence reads. The speed, sensitivity and accuracy of read mapping are crucial to determining the full spectrum of single nucleotide variants (SNVs) as well as structural variants (SVs) in the donor genomes analyzed.Results: We present drFAST, a read mapper designed for di-base encoded 'color-space' sequences generated with the AB SOLiD platform. drFAST is specially designed for better delineation of structural variants, including segmental duplications, and is able to return all possible map locations and underlying sequence variation of short reads within a user-specified distance threshold. We show that drFAST is more sensitive in comparison to all commonly used aligners such as Bowtie, BFAST and SHRiMP. drFAST is also faster than both BFAST and SHRiMP and achieves a mapping speed comparable to Bowtie.