Tutorials for BMS500C 2023 class
The overall objectives of this session are
- to become familiar with navigating in a command-line (Linux) environment.
- to perform basic and more sophisticated command-line operations (such as using regex, piping, and for-loops) to parse and manipuate data.
- to learn the basic operations for performing a reference-based assembly, calling variants, and evaluating the results.
- to generate viral phylogenies for assessing relationships among isolates and looking for temporal and geographical signals.
To achieve these objectives, we will download next-generation sequencing (NGS) data from the Sequence Read Archive (SRA) on NCBI for several West Nile Virus isolates/samples. After mapping the sequence reads to a reference genome, we will generate some summary statistics to evaluate the quality of our assemblies and perform variant analyses to idenfity high-quality single-nucleotide polymorphisms (SNPs). This information will be used to generate consensus genomes for our isolates/samples. We will infer the relationships of our genomes to each other and to other contextual West Nile Virus genomes from North America by generating a phylogeny and evaluating whether there is a geographical and/or temporal signal to the data.
West Nile Virus (WNV) is a vector-borne RNA flavivirus transmitted between mosquito vectors and avian hosts. Introduced into the New York area in 1999, it has since spread throughout the United States and other regions of North America as well as South and Central America. While most people are asymptomatic, the disease can be fatal if the virus enters the central nervous system. The number of cases of WNV is on the rise in the US, at least partially attributable to climate change. The high degree of conservation among WNV genomes (i.e. little evolutionary change) suggests that adaptive changes are constrained due to cycling between vector and host. We will test whether this high level of conservation among WNV genomes obscures geographic and temporal signals.