Dr Matt Field and Dr Ira Cooke

WORKSHOP: Assembling complete bacterial genomes using long-reads

Starting from raw Nanopore long read data we will assemble a complete bacterial genome.  We will cover all major analysis steps including adapter trimming, de novo assembly, assembly quality assessment, polishing, and annotation.

Keywords: Long reads, genome assembly, assembly quality, polishing

Requirements: Web access. Assumes basic familiarity with the assembly process and command line.

Relevance: Suitable for people looking to explore using long reads for de novo genome assembly.

Dr Matt Field

Principal Research Fellow, BioInformatics, Australian Institute of Tropical Health & Medicine, James Cook University

Matt Field is a Principal Senior Research Fellow in Bioinformatics at the Australian Institute of Tropical Health and Medicine at James Cook University. He currently holds an NHMRC CJ Martin Early Career Research Fellowship and was recently awarded the Frank Fenner Early Career Fellowship for the highest scoring ECR applicant. Dr Field is a founder and co-director of the Centre for Tropical Bioinformatics and Molecular Biology and specialises in developing high-throughput bioinformatic analysis pipelines.

In the last five years Dr Field has published 40 peer reviewed publications in high impact journals such as Nature (x2), Cell, Science Advances and PNAS (x2), which have been cited over 3000 times. He is also a Chief Investigator for the Centre for Personalised Immunology, an NHMRC Centre of Research Excellence focused on bringing genomics and personalized medicine into routine clinical practice.

Dr Ira Cooke

Senior Lecturer – Bioinformatics, Australian Institute of Tropical Health & Medicine, James Cook University

As a bioinformatician I can combine my dual interests in molecular biology and computational tools.  My career reflects this crossing of disciplinary boundaries.  After completing my undergraduate studies at JCU in marine biology and chemistry I pursued a PhD in physics at ANU.  After that I worked with Markus Deserno at the Max Planck institute for polymer physics in Germany where I helped develop a model for simulating large scale lipid self assembly.  This was followed by several years in the UK working on economic and ecological models of farmland with Prof. Bill Sutherland.  I returned to Australia in 2010 where I started working as a bioinformatician with the La Trobe University mass spectrometry facility.  I soon realised that bioinformatics was the ideal way for me to combine my various computational and biological interests.  In 2016 I moved to James Cook University where I teach bioinformatics and use bioinformatic tools to answer a wide range of research questions related to molecular biology of marine organisms and tropical diseases.

I am interested in the analysis of large genomic, transcriptomic and proteomic datasets.  I use and develop computational tools that take advantage of this data to discover the role that genomic sequences play in cellular and whole organism biology.  I work on a wide variety of research questions including many related to human and veterinary health as well as aquaculture, coral biology and cephalopod toxins.