A Survey on De Novo Assembly: Algorithms and Systems

PhD Qualifying Examination


Title: "A Survey on De Novo Assembly: Algorithms and Systems"

by

Miss Shuang QIU


Abstract:

De novo assembly is the process of putting together whole genome sequences 
from raw sequencing fragment data. It is the basis for subsequent genome 
analysis, which aims at discovering new species or detecting genetic 
variations.

To assemble a large genome is quite challenging due to the computation 
complexity and rapidly growing volumes. The development of sequencing 
technologies also creates new opportunities as well as new issues.

In this survey, we focus on de novo assembly with NGS 
(next-generation-sequencing) data. We first introduce the de novo assembly 
problem and outline the requirements of genome sequencing technologies and 
characteristics of the raw data. Then, we review the classic assembly 
algorithms based on graph models as well as present the existing parallel 
implementations of assemblers. Finally, we discuss the future directions 
of developing a new parallel and distributed assembler on heterogeneous 
computing platforms.


Date:  			Wednesday, 14 October 2015

Time:                  	2:00pm - 4:00pm

Venue:                  Room 1505
                         Lifts 25/26

Committee Members:	Dr. Qiong Luo (Supervisor)
 			Dr. Wilfred Ng (Chairperson)
 			Dr. Lei Chen
 			Dr. Raymond Wong


**** ALL are Welcome ****