Evaluation of methods for de novo genome assembly from high-throughput sequencing reads reveals dependencies that affect the quality of the results.
Evaluation of methods for de novo genome assembly from high-throughput sequencing reads reveals dependencies that affect the quality of the results.
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DOI：
10.1371/journal.pone.0024182
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发表时间：
2011
期刊：
影响因子：
3.7
通讯作者：
Rigoutsos I
中科院分区：
文献类型：
--
作者：
Haiminen N;Kuhn DN;Parida L;Rigoutsos I
高通量测序技术的最新发展使得低成本测序成为许多基因组分析任务的有吸引力的方法。不断增加的读取长度、不断提高的质量和每次仪器运行的可用序列数量不断增加，使全基因组组装成为一个有吸引力的目标应用。在本文中，我们通过对不同长度和来源的基因组序列的详细研究，结合目前流行的几种组装程序，评估了从短reads（≤100个核苷酸）从头组装基因组的可行性。我们的广泛分析表明，除了测序覆盖率之外，目标基因组的结构、使用的组装程序的身份、平均读取长度和观察到的测序错误率等属性都是影响目标序列在大小和正确性方面可实现的最佳组装的强大变量。
Recent developments in high-throughput sequencing technology have made low-cost sequencing an attractive approach for many genome analysis tasks. Increasing read lengths, improving quality and the production of increasingly larger numbers of usable sequences per instrument-run continue to make whole-genome assembly an appealing target application. In this paper we evaluate the feasibility of de novo genome assembly from short reads (≤100 nucleotides) through a detailed study involving genomic sequences of various lengths and origin, in conjunction with several of the currently popular assembly programs. Our extensive analysis demonstrates that, in addition to sequencing coverage, attributes such as the architecture of the target genome, the identity of the used assembly program, the average read length and the observed sequencing error rates are powerful variables that affect the best achievable assembly of the target sequence in terms of size and correctness.
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影响因子：
3.7
作者：
Zhang W;Chen J;Yang Y;Tang Y;Shang J;Shen B
通讯作者：
Shen B
来自非常短的读物的新型细菌基因组的基因促进组装。
影响因子：
4.3
作者：
Salzberg, Steven L.;Sommer, Daniel D.;Puiu, Daniela;Lee, Vincent T.
通讯作者：
Lee, Vincent T.
影响因子：
9.8
作者：
Church DM;Goodstadt L;Hillier LW;Zody MC;Goldstein S;She X;Bult CJ;Agarwala R;Cherry JL;DiCuccio M;Hlavina W;Kapustin Y;Meric P;Maglott D;Birtle Z;Marques AC;Graves T;Zhou S;Teague B;Potamousis K;Churas C;Place M;Herschleb J;Runnheim R;Forrest D;Amos-Landgraf J;Schwartz DC;Cheng Z;Lindblad-Toh K;Eichler EE;Ponting CP;Mouse Genome Sequencing Consortium
通讯作者：
Mouse Genome Sequencing Consortium
影响因子：
7
作者：
Chaisson, Mark J.;Pevzner, Pavel A.
通讯作者：
Pevzner, Pavel A.
影响因子：
48
作者：
Mavromatis, Konstantinos;Ivanova, Natalia;Kyrpides, Nikos C.
通讯作者：
Kyrpides, Nikos C.