Date of Award
12-2022
Document Type
Dissertation
Degree Name
Doctor of Philosophy (PhD)
Department
School of Computing
Committee Chair/Advisor
Feng Luo
Committee Member
Brian Dean
Committee Member
Pradip Srimani
Committee Member
Rong Ge
Abstract
Knowing the genome sequence of an organism is the essential step toward understanding its genomic and genetic characteristics. Currently, whole genome shotgun (WGS) sequencing is the most widely used genome sequencing technique to determine the entire DNA sequence of an organism. Recent advances in next-generation sequencing (NGS) techniques have enabled biologists to generate large DNA sequences in a high-throughput and low-cost way. However, the assembly of NGS reads faces significant challenges due to short reads and an enormously high volume of data. Despite recent progress in genome assembly, current NGS assemblers cannot generate high-quality results or efficiently handle large genomes with billions of reads. In this research, we proposed a new Genome Assembler based on MapReduce (GAMR), which tackles both limitations. GAMR is based on a bi-directed de Bruijn graph and implemented using the MapReduce framework. We designed a distributed algorithm for each step in GAMR, making it scalable in assembling large-scale genomes. We also proposed novel gap-filling algorithms to improve assembly results to achieve higher accuracy and more extended continuity. We evaluated the assembly performance of GAMR using benchmark data and compared it against other NGS assemblers. We also demonstrated the scalability of GAMR by using it to assemble loblolly pine (~22Gbp). The results showed that GAMR finished the assembly much faster and with a much lower requirement of computing resources.
Recommended Citation
Zhang, Yuehua, "Large Genomes Assembly Using MAPREDUCE Framework" (2022). All Dissertations. 3174.
https://tigerprints.clemson.edu/all_dissertations/3174