[BBC] Edinburgh Genomics 1-day workshop: Oxford Nanopore MinION Sequencing - Data Handling, Analysis and Applications Thursday 10 Dec 2015

[Bert Overduin]

To whom this may concern:

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

*Description:*

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].

This workshop will focus on the handling, analysis and applications of
MinION sequence data. The workshop will be a combination of presentations,
demos and hands-on tutorials. In the hands-on tutorials a wide range of
software programs will be used, some of which were especially developed for
the MinION.

[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 at 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.


With kind regards,
Bert Overduin

-- 
Bert Overduin, PhD
TRAINING AND OUTREACH BIOINFORMATICIAN
Bert.Overduin at ed.ac.uk

EDINBURGH GENOMICS
The University of Edinburgh
Ashworth Laboratories
The King's Buildings
Charlotte Auerbach Road
Edinburgh EH9 3FL
Scotland, United Kingdom

tel. +44(0)1316507403
http://genomics.ed.ac.uk
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