Contribute Media
A thank you to everyone who has made this possible: Read More

Remote DNA Sequencing and Analysis; Nanopore sequencing, FPGA boards and a fortunate Epiphany

Description

What is a MinION?

Oxford Nanopore's MinION is a 91g portable sequencing device, which has been a huge talking point in the sequencing community since entering the market in 2014. First thought of as having potential, it's now recognised as a valuable asset of any genomic laboratory. The MinION can deliver long-read yields as great as its competitor PacBio. This is due to its yield per flowcell increasing 10-fold in the past 18 months, which has created much delight to the community albeit some problems for researchers (and ONT themselves) when it comes to data handling and analysis.

Current Restrictions

The raw output from a MinION is an electrical signal over-time which must be put through a computationally-intensive RNN to infer the nucleotides of a given DNA strand - this process is known as basecalling. If one were to do this on a normal laptop, it would take over a week to complete all the reads from a 48-hour run, which hinders the real-time component of the MinION technology. In order to keep the basecall processing at the same rate as the throughput, the MinION output needs to be transferred to a high powered server, which hinders on the MinION's portability.

How to overcome this?

Running reads simultaneously through this basecalling processing is a must when it comes to real-time Nanopore sequencing, which is why we combine ONT with another start-up project, Adapteva's Parallela board, a credit card sized micro-server with an in-built FPGA board, ideal for parallel processing. We explore the compatability of the Parallela and the MinION, with the aim of performing both sequencing and analysis in a remote environment.

Details

Improve this page