Computing That Serves

De novo Assembly of Large Genomes from Paired Short Reads


Thursday, March 4, 2010 - 11:00am


Srinivas Aluru
Department of Computer Engineering
Iowa State University

For nearly three decades, the Sanger method of reading one DNA sequence at a time served as the mainstay of genomics research. The advent of high-throughput short read DNA sequencing technology is enabling revolutionary advances in life sciences by providing an inexpensive way to sample genomes at high coverage. Assembling such short reads to discover hitherto unsequenced organisms is an important challenge in computational biology. The need for memory-intensive graph based models for accurate assembly coupled with the much larger number and higher coverage needed for short reads, is limiting the reach of serial assemblers. In this talk, I will present our parallel short read assembly framework that can assemble large genomes from high coverage sampling of paired short reads with approximate distance constraints. Our framework can handle multiple sized reads and multiple types of distance constraints. I will demonstrate the applicability of this work in genome sequencing projects and comment on future directions.


Srinivas Aluru is the Mehl Professor of Computer Engineering at Iowa State University, and the Bajaj Chair Professor of Computer Science and Engineering at Indian Institute of Technology Bombay. Earlier, he served as Chair of Iowa State's Bioinformatics and Computational  Biology program, and held faculty positions at New Mexico State University and Syracuse University. Aluru conducts research in high performance computing, bioinformatics and systems biology, combinatorial scientific computing, and applied algorithms. He pioneered the development of parallel methods in computational biology, and contributed to the sequencing and analysis of the maize genome. He is a Fellow of the IEEE, and is a recipient of the NSF Career award, the Swarnajayanti fellowship from the Government of India, IBM faculty award, and Iowa State University Foundation award for mid-career achievement in research.