Conventions used in this thesis

Throughout this thesis, the following naming conventions are used.

• The terms “undetermined” and “unclassified” are used interchangeably.
  
• When referring to a sample, a physical specimen, observation or record is meant.
  
• The elements of high throughput sequencing outputs are the so-called sequencing reads. Here I refer to them as either “sequencing reads” or just “reads” which means the same.