Roary: rapid large-scale prokaryote pan genome analysis
Roary: rapid large-scale prokaryote pan genome analysis
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DOI：
10.1093/bioinformatics/btv421
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发表时间：
2015-11-15
期刊：
影响因子：
5.8
通讯作者：
Parkhill, Julian
中科院分区：
文献类型：
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作者：
Page, Andrew J.;Cummins, Carla A.;Parkhill, Julian
一个典型的原核生物种群测序研究现在可以由数百或数千个分离物组成。研究这些数据集可以提供对原核生物基因组遗传结构的详细见解。我们介绍了Roary，一个快速构建大规模泛基因组的工具，识别核心和辅助基因。Roary可以在标准桌面上构建数千个原核生物样本的泛基因组，而不会影响结果的准确性。使用单个CPU Roary可以使用13gb RAM在4.5小时内生成由1000个分离株组成的泛基因组，使用多个处理器可以进一步加速。
A typical prokaryote population sequencing study can now consist of hundreds or thousands of isolates. Interrogating these datasets can provide detailed insights into the genetic structure of prokaryotic genomes. We introduce Roary, a tool that rapidly builds large-scale pan genomes, identifying the core and accessory genes. Roary makes construction of the pan genome of thousands of prokaryote samples possible on a standard desktop without compromising on the accuracy of results. Using a single CPU Roary can produce a pan genome consisting of 1000 isolates in 4.5 hours using 13 GB of RAM, with further speedups possible using multiple processors.