Developing bioinformatics approaches for the anaylsis of influenza virus whole genome sequence data.

流感病毒对世界各地的人类和动物健康具有关键影响，感染人类和牲畜，并播下流行病的种子。测序技术使我们能够以前所未有的规模监测和了解这些病毒的遗传变异。然而，由于现在可以对数百或数千个病毒全基因组进行常规测序，因此需要新的生物信息学方法来分析和处理这种规模的数据。这一领域的方法学发展对于了解流感病毒如何进化和传播的目的变得越来越重要。流感病毒基因组由8个片段组成，这些片段不断发生突变和重排，导致抗原漂移和抗原漂移。微生物基因组学中的许多标准生物信息学方法是为从进化速度慢得多的细菌获得的数据而设计的。因此，从分类到映射的许多方法都可能表现得不太理想。同时，现代系统动力学方法可以提供重要的信息，但许多方法不是为大数据应用而设计的。该项目专注于开发尖端生物信息学方法和建模，用于处理和分析流感病毒全基因组测序数据，与加的夫大学的世界级研究人员和英国各地的合作者合作。这位学生为整个基因组测序管道的几个部分设计了生物信息学算法和建模方法，包括序列组装、分类和系统动力学建模。

Influenza viruses have a key impact on human and animal health worldwide, infecting humans and livestock and seeding pandemics. Sequencing technologies have enabled us to monitor and understand the genetic variation of these viruses at unprecedented scale. However, since it is now possible to routinely sequence hundreds or thousands of virus whole genomes, new bioinformatics approaches are required for analysis and processing of data at this scale. Methodological development in this area has become increasingly important for the purposes of understanding how influenza viruses evolve and spread. The influenza virus genome is composed of 8 segments which continuously mutate and reassort, which result in antigenic drift and antigenic shift. Many standard bioinformatics approaches in microbial genomics were designed for data derived from bacteria that evolve at a much slower rate. As such, many approaches, from classification to mapping, can perform sub-optimally. Simultaneously, modern phylodynamic methods can provide important information, but many are not designed for big data applications.This project was focused on the development of cutting-edge bioinformatics methods and modelling for the processing and analysis of influenza virus whole genome sequencing data, working with world-class researchers from University of Cardiff and collaborators across the UK. The student designed bioinformatics algorithms and modelling approaches for several parts of the whole genome sequencing pipeline, including sequence assembly, classification, and phylodynamic modelling.