NOVOPlasty: de novo assembly of organelle genomes from whole genome data.
NOVOPlasty: de novo assembly of organelle genomes from whole genome data.
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DOI：
10.1093/nar/gkw955
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发表时间：
2017-02-28
影响因子：
14.9
通讯作者：
Smits G
中科院分区：
文献类型：
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作者：
Dierckxsens N;Mardulyn P;Smits G
下一代测序（NGS）技术的发展导致了许多不同的组装算法的发展，但其中很少有人专注于组装细胞器基因组。这些基因组用于系统发育研究、食品鉴定，是GenBank中保存最多的真核生物基因组。从全基因组测序（WGS）数据中产生细胞器基因组组装将是最准确和最省力的方法，但缺乏专门为此任务设计的工具。我们开发了一种种子和扩展算法，该算法从全基因组测序（WGS）数据中组装细胞器基因组，从相关或遥远的单个种子序列开始。该算法已经在几个新的（Gonioctena intermedia和Avicennia marina）和公共的（拟南芥和水稻）全基因组Illumina数据集上进行了测试，在组装精度和覆盖率方面优于已知的组装器。在我们的基准测试中，NOVOPlasty在不到30分钟的时间内组装了所有测试的圆形基因组，最大内存要求为16 GB，准确率超过99.99%。总之，NOVOPlasty是唯一的从头组装程序，它提供了一个快速和直接的提取的核基因组从WGS数据在一个环形的高质量重叠群。该软件是开源的，可以在https://github.com/ndierckx/NOVOPlasty下载。
The evolution in next-generation sequencing (NGS) technology has led to the development of many different assembly algorithms, but few of them focus on assembling the organelle genomes. These genomes are used in phylogenetic studies, food identification and are the most deposited eukaryotic genomes in GenBank. Producing organelle genome assembly from whole genome sequencing (WGS) data would be the most accurate and least laborious approach, but a tool specifically designed for this task is lacking. We developed a seed-and-extend algorithm that assembles organelle genomes from whole genome sequencing (WGS) data, starting from a related or distant single seed sequence. The algorithm has been tested on several new (Gonioctena intermedia and Avicennia marina) and public (Arabidopsis thaliana and Oryza sativa) whole genome Illumina data sets where it outperforms known assemblers in assembly accuracy and coverage. In our benchmark, NOVOPlasty assembled all tested circular genomes in less than 30 min with a maximum memory requirement of 16 GB and an accuracy over 99.99%. In conclusion, NOVOPlasty is the sole de novo assembler that provides a fast and straightforward extraction of the extranuclear genomes from WGS data in one circular high quality contig. The software is open source and can be downloaded at https://github.com/ndierckx/NOVOPlasty.