Lead Software Engineer
PhD, MEng, BSc
Lead Software Engineer
Scalable Pathogen Pipeline Platform (SP3)
Pathogen genomic data analysis can be extremely bespoke and diverse. I am leading the software development of a Scalable Pathogen Pipeline Platform (SP3), providing an efficient and unified process of collecting, analysing and comparing genomic data analysis with the benefit of elastic cloud computing. The system has been tested on local HPC (Slurm), Google Cloud Platform (GCP), Amazon Elastic Compute Cloud (Amazon EC2), Microsoft Azure and OpenStack Platform. Here is SP3.
ViewBovine: Linking Genetic Relatedness and Geographical Neighbourhood
Bovine tuberculosis (bTB) is endemic in some parts of England and Wales of United Kingdom. The majority of bTB incidents result from direct movement of infected beef fattening animals from endemic bTB areas or from movement of infected animals between infected herds. I have led the development of a web-based interactive visualisation tool, linking the genetic relatedness and geographical neighbourhood for understanding bTB transmission. The web-based interactive visualisation tool, named ViewBovine, dynamically integrates the genetic relatedness data from whole genome sequencing (WGS) analytics and the cattle geographical neighbourhood.
NanoSPC: a scalable, portable, cloud compatible viral nanopore metagenomic data processing pipeline
Here we introduce NanoSPC, a scalable, portable and cloud compatible pipeline for analyzing Nanopore sequencing data. NanoSPC can identify potentially pathogenic viruses and bacteria simultaneously to provide comprehensive characterization of individual samples. The pipeline can also detect single nucleotide variants and assemble high quality complete consensus genome sequences, permitting high-resolution inference of transmission.
NanoSPC: a scalable, portable, cloud compatible viral nanopore metagenomic data processing pipeline.
Xu Y. et al, (2020), Nucleic acids research, 48, W366 - W371
Scalable Pathogen Pipeline Platform (SP^3): Enabling Unified Genomic Data Analysis with Elastic Cloud Computing
Yang-Turner F. et al, (2019), 2019 IEEE 12th International Conference on Cloud Computing (CLOUD)
An Open-Source Azure Solution for Scalable Genomics Workflows
Yang-Turner F. et al, (2018), 2018 IEEE World Congress on Services (SERVICES)