Practical evaluation of 11 de novo assemblers in metagenome assembly
Practical evaluation of 11 de novo assemblers in metagenome assembly
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DOI：
10.1016/j.mimet.2018.06.007
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发表时间：
2018-08-01
影响因子：
2.2
通讯作者：
Yakhchali, Bagher
中科院分区：
文献类型：
--
作者：
Forouzan, Esmaeil;Shariati, Parvin;Yakhchali, Bagher
下一代测序（NGS）技术正在彻底改变生物学和基于宏基因组学的研究领域。由于宏基因组数据量通常非常大，因此从头宏基因组组装可以有效地用于减少数据总量并提高下游分析的质量，例如注释和分箱。虽然有许多免费的汇编器，但选择一个适合特定目标的汇编器可能非常具有挑战性。在这项研究中，11个著名的组装器的性能进行了评估，在三个不同的宏基因组的组装。结果表明，MetaSPAdes是最好的汇编器和Megahit是一个很好的选择保守的组装策略。此外，这项研究提供了有用的信息，每个汇编程序的优点和缺点，以及读取长度对汇编的影响，从而帮助学者选择最佳的汇编程序的基础上，他们的目标。
Next Generation Sequencing (NGS) technologies are revolutionizing the field of biology and metagenomic-based research. Since the volume of metagenomic data is typically very large, De novo metagenomic assembly can be effectively used to reduce the total amount of data and enhance quality of downstream analysis, such as annotation and binning. Although, there are many freely available assemblers, but selecting one suitable for a specific goal can be highly challenging. In this study, the performance of 11 well-known assemblers was evaluated in the assembly of three different metagenomes. The results obtained show that metaSPAdes is the best assembler and Megahit is a good choice for conservative assembly strategy. In addition, this research provides useful information regarding the pros and cons of each assembler and the effect of read length on assembly, thereby helping scholars to select the optimal assembler based on their objectives.