| 基于De Bruijn图的De Novo序列组装软件性能分析 |
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| 作者姓名： | 孟金涛 苑建蕊 魏彦杰 冯圣中 |
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| 作者单位： | 1. 中国科学院先进技术研究院 高性能中心, 广东 深圳 518055;
2. 中南大学 信息科学与工程学院, 湖南 长沙 410083;
3. 长园深瑞继保自动化有限公司, 广东 深圳 518057 |
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| 摘 要： | 随着新一代测序技术的发展，一些新的全基因组组装算法应运而生，特别是针对第三代高通量测序仪产生的海量短序列的组装软件被不断开发出来，这些组装软件渐渐走向市场。但是，由于这些组装软件的适用性和其性能的差别，选择一款性能优良的组装工具或者开发并行高吞吐的组装工具成为了当前面临的一大难题。本文选取基于 De Bruijn 图算法开发的 4 款 De Novo 组装的软件（Velvet、SOAPdenovo、IDBA、ABySS）对 4 种物种的基因组的模拟数据进行测试，并从软件的算法、组装性能和组装质量 3 个方面分析这 4 个软件的性能，同时根据其算法特点推断影响这些软件性能的关键因素，并给出软件的使用建议以及开发并行序列组装工具来组装超大规模的基因数据应该注意的问题。
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| 关 键 词： | 组装软件 De Bruijn 图 DNA 测序技术 性能分析 质量评测 |
| 收稿时间： | 2013-07-11 |
The Analysis of De Novo Genome Assembly Software Based on De Bruijn Graph |
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| Authors: | Meng Jintao Yuan Jianrui Wei Yanjie Feng Shengzhong |
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| Affiliation: | 1. High Performance Computing Center, Shenzhen Institutes of advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China;
2. Department of Computer Science and Technology, Central South University, Changsha, Hunan 410083, China;
3. CYG SUNRI Co., LTD. Shenzhen, Guangdong 518057, China |
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| Abstract: | Recently, new sequencing technologies have emerged, a new set of algorithms have been developed, and several assembly software packages have been created specifically for assembly of next-generation sequencing data. However, due to the poor knowledge about the applicability and performance of these software tools, choosing a befitting assembler becomes a tough task. Here we compare the performance between Velvet, SOAPdenovo, IDBA and ABySS, which all are developed based on De Bruijn graph. We compare computational time, assembly accuracy and integrity, our comparison study will assist researchers in selecting a well-suited assembler and offer essential information for the development of existing assemblers. |
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| Keywords: | assembler software De Bruijn Graph sequencing technology performance analysis quality of contigs |
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