Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de bruijn graphs.
Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de bruijn graphs.
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DOI：
10.1371/journal.pone.0060058
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Maclean D
中科院分区：
文献类型：
--
作者：
Leggett RM;Ramirez-Gonzalez RH;Verweij W;Kawashima CG;Iqbal Z;Jones JD;Caccamo M;Maclean D
单核苷酸多态性是追踪可遗传性状遗传基础的宝贵标记，快速创建标记库的能力对于及时鉴定靶基因至关重要。下一代测序使得快速对基因组进行采样成为可能，但多态性检测依赖于具有可以与读取进行比对并检测到变体的参考基因组。我们提出了Bubbleparse，一种直接从下一代读取中检测变体而无需参考序列的方法。Bubbleparse使用Cortex框架中的de Bruijn图实现作为基础，并允许用户快速，轻松和敏感地识别这些图中代表多态性的气泡。我们发现，Bubbleparse算法是敏感的，可以快速检测到许多多态性，它表现良好，与基于在拟南芥中的参考比对的多态性检测方法相比。我们表明，启发式可以用来最大限度地提高返回的真实多态性的数量，并与原理验证实验表明，Bubbleparse是非常有效的数据从未测序的野生亲缘的马铃薯，使我们能够快速，轻松地识别抗病相关基因。
Single Nucleotide Polymorphisms are invaluable markers for tracing the genetic basis of inheritable traits and the ability to create marker libraries quickly is vital for timely identification of target genes. Next-generation sequencing makes it possible to sample a genome rapidly, but polymorphism detection relies on having a reference genome to which reads can be aligned and variants detected. We present Bubbleparse, a method for detecting variants directly from next-generation reads without a reference sequence. Bubbleparse uses the de Bruijn graph implementation in the Cortex framework as a basis and allows the user to identify bubbles in these graphs that represent polymorphisms, quickly, easily and sensitively. We show that the Bubbleparse algorithm is sensitive and can detect many polymorphisms quickly and that it performs well when compared with polymorphism detection methods based on alignment to a reference in Arabidopsis thaliana. We show that the heuristic can be used to maximise the number of true polymorphisms returned, and with a proof-of-principle experiment show that Bubbleparse is very effective on data from unsequenced wild relatives of potato and enabled us to identify disease resistance linked genes quickly and easily.
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影响因子：
7
作者：
Simpson, Jared T.;Wong, Kim;Birol, Inanc
通讯作者：
Birol, Inanc
使用彩色de bruijn图的从头组装和基因分型。
影响因子：
30.8
作者：
Iqbal, Zamin;Caccamo, Mario;Turner, Isaac;Flicek, Paul;McVean, Gil
通讯作者：
McVean, Gil
DOI：
10.1093/bioinformatics/btp352
发表时间：
2009-08-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Li H;Handsaker B;Wysoker A;Fennell T;Ruan J;Homer N;Marth G;Abecasis G;Durbin R;1000 Genome Project Data Processing Subgroup
通讯作者：
1000 Genome Project Data Processing Subgroup
DOI：
10.1534/g3.111.000240
发表时间：
2011-08
期刊：
G3 (Bethesda, Md.)
影响因子：
--
作者：
Catchen JM;Amores A;Hohenlohe P;Cresko W;Postlethwait JH
通讯作者：
Postlethwait JH
DOI：
10.1093/bioinformatics/btp324
发表时间：
2009-07-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Li H;Durbin R
通讯作者：
Durbin R