Population graph for Mycobacterium Tuberculosis

Population graph for Mycobacterium Tuberculosis

Mouzos, L.

Abeel, T.E.P.M.F. (mentor)

Electrical Engineering, Mathematics and Computer Science

Intelligent Systems

2017-04-11

In recent years, cheap sequencing has resulted in hundreds or thousands of individual genomes available for many species. Therefore, it is logical to rethink the concept of the reference genome; as consisting of a population of genomes rather than being a single one. The term pan-genome describes a population of genomes of the same species or a kingdom of species (Lapierre & Gogarten, 2009) and it was first introduced by Tettelin et. al (2005). More recent studies develop population graphs as alternatives to the single-reference, which seek to encode multiple genomes in a single representation. These graphs attempt to represent the variability of a population in terms of sequence(single nucleotide polymorphisms (SNPs), insertions/deletions (indels))and structural (large inversions and deletions) variations.In this thesis, we sought to represent hundreds of Mycobacterium tuberculosis (MTB) genomes in a graph-representation, including gene annotation. Contrary to the current solutions, we attempt to correct structural inversions, resulting in a more accurate alignment and less redundant representation.

pan-genomics
population graph
Mycobacterium Tuberculosis
structural variations
gene annotations

http://resolver.tudelft.nl/uuid:11f0e772-3564-4e22-b4d7-fe94c6b69987

Student theses

master thesis

(c) 2017 Mouzos, L.