Development of computational strategies for identification and characterisation of viruses in metagenomic samples

元基因组学是研究混合环境样本的DNA，其中包括许多不同生物的基因组。我们可以使用相同的下一代测序技术对元基因组样本进行测序，这与我们用来对单个生物体的基因组进行测序相同，但分析数据要复杂得多，因为很难事先知道样本中存在哪些生物体，因此很难知道特定的DNA片段(读取)来自哪个生物体。组装是将短片段组合成代表更长DNA片段的重叠群的过程，从而实现更有用的分析。当涉及单个生物体的DNA时，组装是一个困难但相对成熟的领域。然而，组装工具所做的许多简化假设在处理元基因组数据时是无效的，这使得元基因组组装过程变得更加困难，该领域更加不成熟。本项目的目的是开发元基因组组装的计算算法，并产生一个敏感的工具，能够准确地区分非常相似的物种。我们瞄准了一种涉及病毒检测的特定类型的元基因组数据，因为这是一个重要的领域，而且由于现有的少量元基因组组装工具，这一领域尤其没有得到充分解决。使用这样的工具，科学家能够从元基因组样本中获得重要信息，包括了解动物和人类的疾病机制，检测新病毒并监测病毒的传播，以预防和遏制疫情。

Metagenomics is the study of the DNA of mixed environmental samples that include the genomes of many different organisms. We can sequence metagenomic samples using the same next generation sequencing technology that we use to sequence the genome of a single organism, but analysing the data is much more complicated because it is difficult to know in advance which organisms are present in a sample and therefore difficult to know which organism a particular fragment of DNA (a 'read') has come from.Assembly is the process of putting together short reads into contigs that represent a much longer fragment of DNA, enabling more useful analysis. Assembly is a difficult but relatively mature field when it involves DNA from a single organism. However, many of the simplifying assumptions made by assembly tools are invalid when dealing with metagenomic data, making the process of metagenomic assembly much harder and the field much less mature.The aim of this project is to develop computational algorithms for metagenomic assembly and to produce a tool that is sensitive and able to accurately differentiate between very similar species. We have targeted a particular type of metagenomic data involving viral detection because this is an important area and one that is particularly under-addressed with the small number of metagenomic assembly tools that already exist. Using such a tool enables scientists to gain vital information from metagenomic samples, including understanding the mechanisms of disease in animals and humans, detecting novel viruses and monitoring the spread of viruses in order to prevent and contain outbreaks.