Wednesday April 12, 2017
Location: CIC Panther Hollow Room
Damla Senol (CMU)
Next-generation sequencing (NGS) technologies have revolutionized and dominated the sequencing market since 2000, owing to their low cost and ability to generate massive amounts of data at a fast speed in parallel. The existence of successful computational tools that can process and analyze this amount of data quickly and accurately is critically important to take advantage of NGS technologies. However, the short read length of NGS technologies causes alignment errors and ambiguities for read mapping, and poses computational challenges to de novo assembly, due to the repetitive sequences in the genome. The demand for sequencing technologies that can produce longer reads has resulted in the emergence of even newer alternative sequencing technologies.
Nanopore sequencing technology has the potential to make other sequencing technologies obsolete with its ability to generate long reads, provide portability and produce real-time data, but high error rates pose a challenge while generating accurate assemblies. The tools used for nanopore sequence analysis are of critical importance as they should overcome the high error rates of the technology. Our goal is to comprehensively analyze the tools for nanopore sequence analysis with the goals of determining their advantages, disadvantages and bottlenecks; providing guidelines for their usages; and also providing potential future works to take better advantage of nanopore sequencing and to overcome its current disadvantage of high error rates.
Damla Senol is a second year PhD student advised by Onur Mutlu and Saugata Ghose. Her research is focused on computer architecture-aware algorithms and tools for bioinformatics applications.