New Contig Creation Algorithm for the de novo DNA Assembly Problem

DNA assembly is among the most fundamental and difficult problems in bioinformatics. Near optimal assembly solutions are available for bacterial and small genomes, however assembling large and complex genomes especially the human genome using Next-Generation-Sequencing (NGS) technologies is shown to be very difficult because of the highly repetitive and complex nature of the human genome, short read lengths, uneven data coverage and tools that are not specifically built for human genomes. Moreover, many algorithms are not even scalable to human genome datasets containing hundreds of millions of short reads. The DNA assembly problem is usually divided into several subproblems including DNA data error detection and correction, contig creation, scaffolding and contigs orientation; each can be seen as a distinct research area. This thesis specifically focuses on creating contigs from the short reads and combining them with outputs from other tools in order to obtain better results. Three different assemblers including SOAPdenovo [Li09], Velvet [ZB08] and Meraculous [CHS+11] are selected for comparative purposes in this thesis. Obtained results show that this thesis’ work produces comparable results to other assemblers and combining our contigs to outputs from other tools, produces the best results outperforming all other investigated assemblers.

Burgoyne Centre for Entrepreneurship fonds

An Entrepreneurship Centre was established at Brock University in 1988 as a joint venture between the University and the City of St. Catharines. In Januaray 1989, a generous donation was made to the Centre by the Burgoyne family, proprietors of the St. Catharines Standard. The Centre subsequently became known as the Burgoyne Centre for Entrepreneurship (BCE). The Centre’s mission was to “promote excellence in research, education and training for entrepreneur development and new venture creation”. To achieve this objective, it was necessary for the BCE to become a community focal point and serve as a link between academic, private and government sectors in the Niagara Region that were involved in entrepreneurial activities. This was primarily done with the provision of educational programs offered through cooperating organizations. Funding for the Centre came from multiple sources, including fees for services and contract research, endowments and grants, as well as Brock University. An Advisory Council, composed of local prominent businesspeople and chaired by Henry Burgoyne, assisted the Centre with promotion and fundraising. The partnerships established by the BCE with other community bodies such as the Lincoln County Board of Education and the Niagara Region Development Corporation resulted in important collaborative community initiatives such as the Niagara Enterprise Agency and the New Enterprise Store. Such collaborations increased the Centre’s profile without duplicating or competing with services offered by existing agencies. The BCE was also instrumental in establishing an entrepreneurship curriculum for secondary school students, and collaborated with the Faculty of Education at Brock University to offer an Ontario Secondary School Entrepreneurship Specialist Teaching Certificate Program to teachers. As the BCE became more prolific in the community, and the iniatives it fostered in the community began to thrive, the Centre’s leadership required the authority to make instantaneous decisions. This was at odds with the hierarchical structure of the University, to which the BCE was accountable. Ultimately, this situation led to the demise of the Centre. The university focused its efforts on academic research and undergraduate courses, while the community partners took responsibility for any joint programs.