III: Small: Collaborative Research: A Scalable and Efficient Optical Map Assembler

Principal Investigator: Christina Boucher

Sponsor: National Science Foundation

Start Date: October 1, 2016

End Date: September 30, 2020

Amount: $383,961

Abstract

Optical mapping is a laboratory technique for constructing ordered high-resolution optical maps from stained molecules of DNA. The popularity of this type of data has amplified because the commercial production of the data has improved in terms of quality, expense, and throughput. For example, BioNano Genomics released a new generation of optical mapping technology called the Irys System in 2015, which has been used to uncover diploid variation in the human genome. However, the raw optical mapping data, called Rmaps, is not inherently useful by itself and must be first assembled into a genome-wide optical map; a computational process that has very few nonproprietary solutions. The optical map assembly problem that aims to stitch together the Rmap data into a genome-wide optical map has some similarities to genome assembly that aims to build contiguous sequences corresponding to the genome of interest from short sequence reads. Although this similarity exists, there are some significant differences that have prevented the direct application of genome assemblers to this latter problem. The main objective of this proposed work is to build a scalable and efficient optical map assembler through the exploration and adaptation of genome assembly algorithms and methods. This research objective will be enhanced by an education plan that aims to broaden the participation in computer science by creating research opportunities for female graduate students, as well as, high school senior students. The plan is to redevelop the existing bioinformatics graduate course so that it: (1) can be cross-listed with the Department of Biology and thus, increase the female enrollment, and (2) will be project based and thus, produce supportive relationships between female students. The team will conduct comprehensive surveys of graduate students in the redeveloped course, as well as the other graduate courses in computer science, to determine whether the changes are impactful. We plan to disseminate our findings to other institutions.

More Information: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1618814&HistoricalAwards=false