PoreCamp Australia 2017

A bootcamp to learn about operating the Oxford Nanopore MinION

PoreCampAU Speakers

Joshua Quick (UK)

Biography

After undergraduate study Joshua worked for Illumina Technologies as intergration scientist. Before
commencing his his PhD at the University of Birmingham, UK.
Joshua is a founder of PoreCamp along with his supervisor Nick Loman.
Throughout his PhD, Joshua has been able to show many successful
applications of real-time nanopore sequencing as demonstrated in the publications below.
Biography source

Publications

A reference bacterial genome dataset generated on the MinION &trade portable single-molecule nanopore sequencer.
Real-time, portable genome sequencing for Ebola surveillance.
Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella.
A complete bacterial genome assembled de novo using only nanopore sequencing data.

David Eccles (NZ)

Abstract

After the stampede of sequenced reads, when the QC dust has settled and the mapping has been done,
it's time to explore the jungle of data provided by the MinION. You will be guided through the process of
pulling out signal from the noise, using MinION reads for variant detection and error correction, and shown
how these discoveries can be presented in a way that is easy to understand.

Biography

David Eccles is a freelance bioinformatician who has worked (mostly remotely) for a number of different researchers
around the world. He is currently working out of an office at the Malaghan
Institute of Medical Research
, where he has been learning about immunology, flow cytometry,
and the all the things that can go wrong with the MinION sequencing device.

David's first placement as a conference speaker was talking about MinION sequencing at the 2015 NGS conference
in New Zealand, which led to a TEDxWellington
talk
in March 2016 where he did sequencing on stage from a tomato source.

Publications

MinION nanopore sequencing of an influenza genome
MinION Analysis and Reference Consortium: Phase 1 data release and analysis

Minh Duc Cao (AU)

Biography

Dr Minh Duc Cao is a senior research officer at Institute for Molecular Bioscience at The University of Queensland.
He completed his PhD in Bioinformatics at Monash University where he applied statistics and information theory
into modelling genomics data. His current research lies in using high‐throughput sequencing data to investigate
genomic variation. Since the introduction of nanopore sequencing technology, he has been developing streamline
algorithms for analysing its data, which take the advantage of ``sequencing in real‐time" while being able to
handle the high error rates of the data.

Publications

Scaffolding and Completing Genome Assemblies in Real-time with Nanopore Sequencing
MStreaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinION sequencing
Realtime analysis and visualization of MinION sequencing data with npReader

Alexa McIntyre (US)

Abstract

As the lengths of spaceflights and the distances of their destinations increase,
portable sequencing will aid in onboard research, environmental sampling,
and infectious disease diagnosis. In collaboration with NASA,
we ran the first demonstrations of MinION use during a parabolic flight and on the International Space Station.
Six onboard experiments generated over 200,000 reads with mean 2D read
accuracies of 85 to 90% for a three-species library, sufficient to assemble lambda phage and E. coli genomes.
Using current signals, we also developed methods to detect the most common bacterial base modification, m6A.
Comparisons to simultaneous terrestrial experiments show that there are no impairments to instrument function
or the quality of data in space and pave the way for further use.

Biography

Alexa is a PhD student in Computational Biology at Weill Cornell Medicine in New York City researching base
modifications in bacteria and viruses. As part of Christopher Mason’s Lab,
she has been analyzing data from NASA’s nanopore sequencing tests on the International Space Station.
She is now working on methods for base modification detection from MinION data.

Publications

Nanopore sequencing in microgravity Nanopore DNA Sequencing and Genome Assembly on the International Space Station