Edinburgh Genomics is happy to offer a 1-day workshop "Oxford Nanopore MinION Sequencing - Data Handling, Analysis and Applications".

Nanopore sequencing is one of the newest sequence technologies, in which single DNA molecules are sequenced directly, without the need for an intervening PCR amplification step or a chemical labelling step. It offers the potential of read lengths of tens of kilo bases.

The Oxford Nanopore MinION (https://www.nanoporetech.com/products-services/minion-mki) is a portable sequencing device that already has proven its power in e.g. the rapid identification of viral pathogens, the monitoring of ebola, genome assembly improvement, and environmental and food safety monitoring. As a member of the pre-release MinION Access Programme (MAP), Edinburgh Genomics has considerable experience in both generating and analyzing MinION sequence data and also has published one of the first software tools to visualize and analyze these data [1].

[1] M Watson et al. poRe: an R package for the visualization and analysis of nanopore sequencing data. Bioinformatics. 2015 Jan 1;31(1):114-5.

Topics:

The following topics will be covered:

• Introduction to the Oxford Nanopore MinION sequencing technology
  
• Organisation of raw reads (poRe/Poretools)
  
• Extraction of FASTQ/A data (poRe/Poretools)
  
• Gathering and visualization of run statistics (poRe/Poretools)
  
• Error correction and quality control (Nanocorr, NanoOK)
  
• Alignment of reads (Last, BWA, R)
  
• Event alignment (Nanopolish)
  
• Scaffolding of short reads (SSPACE-LongRead)
  
• Hybrid de novo assembly (SPAdes)

Who should attend?

This workshop is aimed at anyone who is working with, or is planning to work with, Oxford Nanopore MinION sequence data.

Instructors:

• Mick Watson (Head of Bioinformatics)
  
• Judith Risse (Bioinformatician, Edinburgh Genomics)
  
• Bert Overduin (Training and Outreach Bioinformatician, Edinburgh Genomics)

Requirements:

For this workshop basic knowledge of Linux is essential, while familiarity with R would be advantageous.

Cost:

The registration fee for this workshop is £155, which includes lunch and refreshments.

Application:

You can apply for this workshop by filling in the application form at https://www.surveymonkey.com/r/8WM7SF3. Application will close on Thursday 12 November 2015 noon. Successful applicants will be notified a.s.a.p. after this date.

Information:

For more information, please contact Bert Overduin (bert.overduin@ed.ac.uk).

Note that registration is also open for our RNA-seq, Linux and Python workshops. For more information, please see https://genomics.ed.ac.uk/events/workshops.

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