Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.
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DOI：
10.1186/2047-217x-2-10
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发表时间：
2013-07-22
期刊：
影响因子：
9.2
通讯作者：
Korf IF
中科院分区：
文献类型：
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作者：
Bradnam KR;Fass JN;Alexandrov A;Baranay P;Bechner M;Birol I;Boisvert S;Chapman JA;Chapuis G;Chikhi R;Chitsaz H;Chou WC;Corbeil J;Del Fabbro C;Docking TR;Durbin R;Earl D;Emrich S;Fedotov P;Fonseca NA;Ganapathy G;Gibbs RA;Gnerre S;Godzaridis E;Goldstein S;Haimel M;Hall G;Haussler D;Hiatt JB;Ho IY;Howard J;Hunt M;Jackman SD;Jaffe DB;Jarvis ED;Jiang H;Kazakov S;Kersey PJ;Kitzman JO;Knight JR;Koren S;Lam TW;Lavenier D;Laviolette F;Li Y;Li Z;Liu B;Liu Y;Luo R;Maccallum I;Macmanes MD;Maillet N;Melnikov S;Naquin D;Ning Z;Otto TD;Paten B;Paulo OS;Phillippy AM;Pina-Martins F;Place M;Przybylski D;Qin X;Qu C;Ribeiro FJ;Richards S;Rokhsar DS;Ruby JG;Scalabrin S;Schatz MC;Schwartz DC;Sergushichev A;Sharpe T;Shaw TI;Shendure J;Shi Y;Simpson JT;Song H;Tsarev F;Vezzi F;Vicedomini R;Vieira BM;Wang J;Worley KC;Yin S;Yiu SM;Yuan J;Zhang G;Zhang H;Zhou S;Korf IF
生成原始基因组序列数据的过程继续变得更便宜，更快，更准确。然而，将这些数据组装成高质量的成品基因组序列仍然具有挑战性。许多基因组组装工具是可用的，但它们在性能（速度，可扩展性，硬件要求，接受新的读取技术）和最终输出（组装序列的组成）方面存在很大差异。更重要的是，目前还不清楚如何最好地评估组装基因组序列的质量。Assemblathon竞赛旨在评估基因组组装中的当前最先进方法。在Assemblathon 2中，我们提供了三种脊椎动物物种（鸟，鱼和蛇）的各种序列数据。结果，21个参赛队共提交了43个组件。我们使用光学地图数据，Fosmid序列和几种统计方法的组合来评估这些组件。从100多个不同的指标中，我们选择了10个关键指标来评估组件的整体质量。许多当前的基因组组装器产生有用的组装，包含其基因和整体基因组结构的重要表示。然而，条目之间的高度可变性表明，在基因组组装领域仍有很大的改进空间，并且在组装一个物种的基因组方面工作良好的方法不一定适用于另一个物种。
The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Many current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.