Gastrointestinal Bacteria Reference Unit, National Infections Service, Public Health England, London, UK.
Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.
Bioinformatics. 2018 Sep 1;34(17):3028-3029. doi: 10.1093/bioinformatics/bty212.
Real-time surveillance of infectious disease using whole genome sequencing data poses challenges in both result generation and communication. SnapperDB represents a set of tools to store bacterial variant data and facilitate reproducible and scalable analysis of bacterial populations. We also introduce the 'SNP address' nomenclature to describe the relationship between isolates in a population to the single nucleotide resolution. We announce the release of SnapperDB v1.0 a program for scalable routine SNP analysis and storage of microbial populations.
SnapperDB is implemented as a python application under the open source BSD license. All code and user guides are available at https://github.com/phe-bioinformatics/snapperdb. Reference genomes and SnapperDB configs are available at https://github.com/phe-bioinformatics/snapperdb_references.
使用全基因组测序数据进行实时传染病监测在结果生成和交流方面都存在挑战。SnapperDB 代表了一组工具，用于存储细菌变异数据，并促进细菌群体的可重复和可扩展分析。我们还引入了“SNP 地址”命名法来描述种群中分离物与单核苷酸分辨率之间的关系。我们宣布发布 SnapperDB v1.0，这是一个用于可扩展常规 SNP 分析和微生物种群存储的程序。
SnapperDB 作为一个在开源 BSD 许可证下的 Python 应用程序实现。所有代码和用户指南都可在 https://github.com/phe-bioinformatics/snapperdb 上获得。参考基因组和 SnapperDB 配置可在 https://github.com/phe-bioinformatics/snapperdb_references 上获得。
