Nanopore DNA sequencing is a 3rd generation DNA sequencing approach. The significance of this method, it measures characteristic disruptions in the electric current(raw signal) when DNA passes through a biological nanopore. Then it uses probabilistic models to map raw signal to DNA bases(referred to as base-calling).

ABEA is a prominent algorithm which is used under nanopolish software package in Oxford nanopore DNA sequencing to correct base-calling errors. ABEA is the most time consuming step in Oxford nanopore DNA sequencing(takes about 70% of the total CPU time).

In this study, we optimised and parallelised the ABEA algorithm to run on Field Programming Gate Arrays(FPGA).

Supervisors

• Prof. Roshan Ragel [Scholar]
• Dr. Hasindu Gamaarachchi [Scholar]

Team Members

• Pubudu Premathilaka
• Suneth Samarasinghe
• Wishma Herath