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Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome.外显子组测序鉴定出 MLL2 突变是歌舞伎综合征的一个病因。
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Detection and characterization of novel sequence insertions using paired-end next-generation sequencing.利用配对末端新一代测序技术检测和描述新型序列插入。
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双碱基编码读取的敏感快速映射。

Sensitive and fast mapping of di-base encoded reads.

机构信息

Department of Genome Sciences, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195-5065, USA.

出版信息

Bioinformatics. 2011 Jul 15;27(14):1915-21. doi: 10.1093/bioinformatics/btr303. Epub 2011 May 17.

DOI:10.1093/bioinformatics/btr303
PMID:21586516
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC3129524/
Abstract

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.

AVAILABILITY

The source code for drFAST is available at http://drfast.sourceforge.net

摘要

动机

发现高通量测序基因组之间的差异依赖于序列读取的高效和有效映射。读取映射的速度、灵敏度和准确性对于确定供体基因组中全谱单核苷酸变体 (SNV) 以及结构变体 (SV) 至关重要。

结果

我们提出了 drFAST，这是一种针对 AB SOLiD 平台生成的双碱基编码“颜色空间”序列的读取映射器。drFAST 专门设计用于更好地区分结构变体，包括片段重复，并能够返回用户指定距离阈值内短读取的所有可能的映射位置和潜在的序列变异。我们表明，与所有常用的比对器（如 Bowtie、BFAST 和 SHRiMP）相比，drFAST 更敏感。drFAST 也比 BFAST 和 SHRiMP 快，并且达到了与 Bowtie 相当的映射速度。

可用性

drFAST 的源代码可在 http://drfast.sourceforge.net 获得。