Treangen Todd J, Ondov Brian D, Koren Sergey, Phillippy Adam M
Genome Biol. 2014;15(11):524. doi: 10.1186/s13059-014-0524-x.
Whole-genome sequences are now available for many microbial species and clades, however existing whole-genome alignment methods are limited in their ability to perform sequence comparisons of multiple sequences simultaneously. Here we present the Harvest suite of core-genome alignment and visualization tools for the rapid and simultaneous analysis of thousands of intraspecific microbial strains. Harvest includes Parsnp, a fast core-genome multi-aligner, and Gingr, a dynamic visual platform. Together they provide interactive core-genome alignments, variant calls, recombination detection, and phylogenetic trees. Using simulated and real data we demonstrate that our approach exhibits unrivaled speed while maintaining the accuracy of existing methods. The Harvest suite is open-source and freely available from: http://github.com/marbl/harvest.
现在已有许多微生物物种和进化枝的全基因组序列，然而现有的全基因组比对方法在同时进行多个序列的序列比较方面能力有限。在此，我们展示了用于快速同时分析数千个种内微生物菌株的核心基因组比对和可视化工具的Harvest套件。Harvest包括快速核心基因组多比对器Parsnp和动态可视化平台Gingr。它们共同提供交互式核心基因组比对、变异检测、重组检测和系统发育树。使用模拟数据和真实数据，我们证明我们的方法在保持现有方法准确性的同时展现出无与伦比的速度。Harvest套件是开源的，可从以下网址免费获取：http://github.com/marbl/harvest。
