Computational methods for fast, lightweight and live nanopore sequencing analysis

Third generation Nanopore sequencing is an emerging technology that has countless applications in fields such as precision medicine, forensics and agriculture. While handheld portable nanopore sequencing devices exist, powerful computers are required to perform subsequent data analysis.  This project aims to create improved, highly efficient analysis methods and designs for the future creation of custom computer hardware for portable nanopore analysis. Work involves the design of new algorithms and data structures that maps well to modern computer systems and accelerating those using technologies such as SIMD, GPU, and FPGA. Candidates are expected to have a strong background in computer engineering with a focus on low-level system programming (must be proficient in C), computer architecture and embedded systems. Previous bioinformatics knowledge is not a must but candidates should be prepared to learn the necessary background material quickly. Candidates will be based in the School of Computer Science & Engineering, UNSW Sydney, Australia. Candidates will also collaborate with the Garvan Institute of Medical Research to evaluate their completed systems for real-world applications.

Scholarship

You will need to apply for a UNSW central scholarship: $37,684 per annum (2024 rate, indexed). 

Eligibility

• Domestic and International candidates
• PhD only

How to apply

Email a copy of your CV to Hasindu Gamaarachchi at hasindu+hdr@unsw.edu.au. In emails you send, make sure to include the ASCII text of the following byte array as the subject (not the byte array, but the ASCII text version). This is to make sure I do not miss emails from genuine and serious candidates amongst hundreds of generic spam emails.

80,0x68,68,32,0b1101111,0x70,112,111,114,116,117,110,105,116,0b1111001,32,105,110,0x20,0x66,97,0x73,116,

32,110,97,110,111,112,0b1101111,114,101,32,97,110,0x61,108,121,115,105,115,32,40,118,48,46,49,46,48,41

If you are shortlisted for this project, you will be required to submit a formal application for admission and a UNSW central scholarship.