Scalable Methods for Genome Assembly

Student: Priyanka Ghosh (Washington State University)
Advisor: Ananth Kalyanaraman (Washington State University)

Abstract: Genome assembly is a fundamental problem in the field of bioinformatics wherein the goal lies in the reconstruction of an unknown genome from short DNA fragments obtained from it. With the advent of high-throughput sequencing technologies, billions of reads can be generated in a few hours. My reseach deals with addressing the challenges of conducting genome assembly at scale and developing new methods for conducting extreme-scale genome assembly suited for microbial genomes, and complex eukaryotic genomes. Our approach to the problem is two-fold, wherein we target fast and space-efficient assemblies of moderate sized genomes on a single node with our shared-memory based implementation (FastEtch). Secondly we aim to tackle the assembly of very large genomes with our distributed-memory based approach (PaKman), in an attempt to minimize the turnaround time such that it could potentially pave the way to conducting the assembly process in real-time.

Summary: pdf
Thesis Canvas: pdf



Back to Doctoral Showcase Archive Listing