Repetitive DNA and next-generation sequencing: computational challenges and solutions

被引：1114

作者：

Treangen, Todd J. ^{[1
]}

Salzberg, Steven L. ^{[1
,2
]}

机构：

[1] Johns Hopkins Univ, Sch Med, McKusick Nathans Inst Genet Med, Baltimore, MD 21205 USA

[2] Johns Hopkins Bloomberg Sch Publ Hlth, Dept Biostat, Baltimore, MD 21205 USA

来源：

NATURE REVIEWS GENETICS | 2012年 / 13卷 / 01期

关键词：

RNA-SEQ DATA; COPY NUMBER; COMBINATORIAL ALGORITHMS; SEGMENTAL DUPLICATION; STRUCTURAL VARIATION; SPLICE JUNCTIONS; SNP DISCOVERY; GENOME; ALIGNMENT; REVEALS;

D O I：

10.1038/nrg3117

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

Repetitive DNA sequences are abundant in a broad range of species, from bacteria to mammals, and they cover nearly half of the human genome. Repeats have always presented technical challenges for sequence alignment and assembly programs. Next-generation sequencing projects, with their short read lengths and high data volumes, have made these challenges more difficult. From a computational perspective, repeats create ambiguities in alignment and assembly, which, in turn, can produce biases and errors when interpreting results. Simply ignoring repeats is not an option, as this creates problems of its own and may mean that important biological phenomena are missed. We discuss the computational problems surrounding repeats and describe strategies used by current bioinformatics systems to solve them.

引用

页码：36 / 46

页数：11

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