14th May 2015 - London Calling
In this talk I will cover the highs and lows of being part of the Oxford Nanopore MinION Access Programme. Our laboratory joined the MAP programme in May 2014. Soon afterwards we published the first nanopore read (viewed >4000 times on FigShare) and we released a toolkit for analysing MinION squiggle data (poretools). We piloted the use of nanopore in an large hospital outbreak of Salmonella and demonstrated the utility of real-time sequencing. In September we released a large reference dataset of E. coli K-12 which was used as a reference dataset for bioinformatics algorithm development, and we managed to produce a de novo assembly from these data alone. Now we are turning our attention to using the MinION nearer the patient and in more remote locations for the purposes of outbreak epidemiology and metagenomics diagnostics. Challenges include shrinking the molecular laboratory into a backpack, reducing DNA inputs and developing new software for rapid data analysis.