Consensus software approach in bioinformatics workflows

Given the complexity of incorporating external software into bioinformatics workflows, a tendency exists to rely on the results from a single tool alone. While identifying and integrating the single best performing tool for an application is often sufficient, there are scenarios where running multiple tools and taking the consensus is preferable. In this talk, I will consider the suitability of the consensus approach within common bioinformatic workflows including RNA-Seq, variant detection, and metagenomics. I will demonstrate that while implementing a consensus approach represents an increase in complexity and computation the results offer indisputable improvements in data quality.  Finally, I will discuss the general properties of applications most likely to benefit from this approach.

Speaker bio:

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.

From 2010 to 2015 Dr Field worked as Senior Bioinformatics Manager at the Australian National University, developing software to uncover the underlying genetic cause of human diseases such as lupus, diabetes, and melanoma. During this time he developed a high-throughput variant detection pipeline which has analysed over 4000 exomes and 3000 genomes to date. He completed a PhD at ANU in medical science titled "Computational Analysis of Genetic Variation" with supervisor Chris Goodnow. From 2004 to 2010 Dr Field worked as Assistant Bioinformatic Coordinator at the Genome Sciences Centre in Canada leading a group of bioinformaticians in a high-throughput research environment studying a variety of cancers. Prior to this, he completed two Bachelor of Science degrees in computer science and biology from the University of British Columbia.