19-BBSRC-NSF/BIO genomeRxiv: a microbial whole-genome database & diagnostic marker design resource for classification, identification & data sharing

准确识别对社会和环境产生影响的微生物，除了为理解微生物学提供可靠的经验核心外，还是维持健康的社会和健康的环境以及抗击疾病的先决条件。DNA测序革命创造了利用培养和未培养微生物的基因组序列进行快速准确鉴定的机会。然而，如果没有参考数据库来精确地界定具有独特特征的微生物类别，准确的识别是不可能的，而如果没有快速算法来处理被测序的大量基因组序列，快速识别是不可能的。因此，我们将加强我们现有的网络服务器，以开发genomeRxiv，它将提供一个包含数十万准确编目和分类的公共基因组序列的数据库，仅基于其基因组序列就为基础和应用研究社区提供精确和准确的未知分离株识别。一个独特的新功能将是为学术、工业和政府社区提供识别和宣布测序基因组的能力，而不必共享序列本身，为商业和伦理敏感的生物(例如生产工程菌株、潜在的生物武器，以及与土著社区分享利益)提供保密。GenomeRxiv还将通过提供设计分子诊断工具的能力来实现其分类方案的实际应用，以直接在环境中检测特定的细菌组，包括高影响微生物。通过利用我们已经开发的计算工具和平台并将它们集成到新的网络服务器中，我们在开发genomeRxiv方面处于独特的地位。我们将把高度可分辨的生命识别号分类框架(PI Vinazter和Heath)、Sourmash的速度和计算效率(Pi Brown)以及PYANI(Pi Pritchard)的精确度和过滤能力与LINbase Web服务器的协作众包框架(Pis Vinazter和Heath)结合起来。

Precise identification of microorganisms that impact on society and the environment is a prerequisite for maintaining a healthy society and a healthy environment and for combating diseases, in addition to providing a sound empirical core for understanding microbiology. The DNA sequencing revolution has created the opportunity to use genome sequences of cultured and uncultured microorganisms for fast and precise identification. However, precise identification is impossible without reference databases that precisely circumscribe classes of microorganisms with their unique characteristics, and rapid identification is impossible without fast algorithms that can handle the deluge of genome sequences being sequenced. Therefore, we will enhance our current web server to develop genomeRxiv, which will provide a database of hundreds of thousands of accurately catalogued and classified public genome sequences supplying the basic and applied research community with precise and accurate identification of unknown isolates based on their genome sequences alone.A unique new feature will be provision of the academic, industrial, and government communities with the ability to identify, and announce, sequenced genomes without having to share sequences themselves, providing confidentiality for commercially- and ethically-sensitive organisms (e.g. production engineering strains, potential bioweapons, and benefit sharing with indigenous communities). genomeRxiv will also enable practical application of its classification scheme by providing the capability to design molecular diagnostic tools to detect specific groupings of bacteria, including high impact microorganisms, directly in the environment.We are uniquely placed to develop genomeRxiv by leveraging the computational tools and platforms that we have already developed and by integrating them into the new web server. We will combine the highly-resolved classification framework of Life Identification Numbers (PIs Vinazter and Heath), the speed and computational efficiency of sourmash (PI Brown), and the precision and filtering of pyani (PI Pritchard), with the collaborative crowdsourcing framework of the LINbase web server (PIs Vinazter and Heath).