Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads.
Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads.
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DOI：
10.1101/gr.170720.113
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发表时间：
2014-08
期刊：
影响因子：
7
通讯作者：
Itoh T
中科院分区：
文献类型：
--
作者：
Kajitani R;Toshimoto K;Noguchi H;Toyoda A;Ogura Y;Okuno M;Yabana M;Harada M;Nagayasu E;Maruyama H;Kohara Y;Fujiyama A;Hayashi T;Itoh T
尽管最近已经使用高通量测序仪进行了许多从头基因组组装项目，但由于主要使用的de Bruijn图结构的复杂性增加，组装高度杂合的二倍体基因组是一个巨大的挑战。为了解决对非模型和/或野生型样品测序的日益增长的需求，在大多数情况下，使用近交系或基于fosmid的分级测序方法来克服这些问题。然而，这些方法成本高且耗时，丧失了大规模并行测序的优势。在这里，我们描述了一种新的从头组装，悬铃木，可以有效地管理高通量数据杂合样本。悬铃木通过构建de Bruijn图将DNA片段（读段）组装成重叠群，该de Bruijn图具有自动优化的k-mer大小，然后基于配对末端信息构建重叠群的支架。由杂合性产生的复杂图结构不仅在重叠群组装步骤期间而且在支架步骤期间被简化。我们评估了具有不同杂合性水平的真核样品的组装结果。与其他组装器相比，Platanus产生的组装结果具有更大的支架NG 50长度，而在模拟和真实的数据中没有任何伴随的准确性损失。此外，悬铃木记录了在从头组装竞赛中使用的三个低杂合性物种中的两个的最大支架NG 50值，组装子2。因此，悬铃木提供了一种新的和有效的方法来组装千兆碱基大小的高度杂合的基因组，是一个有吸引力的替代现有的组装设计的基因组的较低的杂合性。
Although many de novo genome assembly projects have recently been conducted using high-throughput sequencers, assembling highly heterozygous diploid genomes is a substantial challenge due to the increased complexity of the de Bruijn graph structure predominantly used. To address the increasing demand for sequencing of nonmodel and/or wild-type samples, in most cases inbred lines or fosmid-based hierarchical sequencing methods are used to overcome such problems. However, these methods are costly and time consuming, forfeiting the advantages of massive parallel sequencing. Here, we describe a novel de novo assembler, Platanus, that can effectively manage high-throughput data from heterozygous samples. Platanus assembles DNA fragments (reads) into contigs by constructing de Bruijn graphs with automatically optimized k-mer sizes followed by the scaffolding of contigs based on paired-end information. The complicated graph structures that result from the heterozygosity are simplified during not only the contig assembly step but also the scaffolding step. We evaluated the assembly results on eukaryotic samples with various levels of heterozygosity. Compared with other assemblers, Platanus yields assembly results that have a larger scaffold NG50 length without any accompanying loss of accuracy in both simulated and real data. In addition, Platanus recorded the largest scaffold NG50 values for two of the three low-heterozygosity species used in the de novo assembly contest, Assemblathon 2. Platanus therefore provides a novel and efficient approach for the assembly of gigabase-sized highly heterozygous genomes and is an attractive alternative to the existing assemblers designed for genomes of lower heterozygosity.
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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
7
作者：
Vinson, JP;Jaffe, DB;Lander, ES
通讯作者：
Lander, ES
DOI：
10.1093/dnares/dss005
发表时间：
2012-04
期刊：
DNA research : an international journal for rapid publication of reports on genes and genomes
影响因子：
--
作者：
Takeuchi T;Kawashima T;Koyanagi R;Gyoja F;Tanaka M;Ikuta T;Shoguchi E;Fujiwara M;Shinzato C;Hisata K;Fujie M;Usami T;Nagai K;Maeyama K;Okamoto K;Aoki H;Ishikawa T;Masaoka T;Fujiwara A;Endo K;Endo H;Nagasawa H;Kinoshita S;Asakawa S;Watabe S;Satoh N
通讯作者：
Satoh N
影响因子：
7
作者：
Li, Ruiqiang;Zhu, Hongmei;Wang, Jun
通讯作者：
Wang, Jun
影响因子：
3.1
作者：
Haussler, David;O'Brien, Stephen J.;Turner, Steve
通讯作者：
Turner, Steve