Oxford Nanopore MinION Sequencing - Data Handling, Analysis and Applications


NOTE: As many aspects of MinION bioinformatics are changing at the moment and we don't want to teach anything that will be soon obsolete, this workshop will most likely not be offered until the end of 2017 at the earliest.

Date:

to be determined

Venue:

The King's Buildings, The University of Edinburgh, Edinburgh, Scotland, UK

Application deadline:

to be determined

Cancellation deadline:

to be determined

Places:

12 (selection of applicants)

Registration fee:

to be determined

Information:

Bert Overduin


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 kilobases. The Oxford Nanopore MinION 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 (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).


"I liked this course - it's a good, well-rounded primer for this subject area." (January 2016)


Instructors

Dr. Judith Risse (Bioinformatician, Wageningen University, The Netherlands)
Dr. Rob Stewart (Bioinformatician, The Roslin Institute)

Workshop format

The workshop consists 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.

Who should attend

Graduates, postgraduates, or PIs, who are working with, or are planning to work with, Oxford Nanopore MinION sequence data.

Requirements

Basic knowledge of Linux is absolutely essential, while some familiarity with R would be advantageous.


Covered topics

Introduction to the Oxford Nanopore MinION sequencing technology
Review of software
Base calling and live statistics
Browsing file content
Extraction of FASTQ/A data
Extraction and analysis of events data
Gathering and visualization of run statistics, and quality control
Alternative base callers
Alignment, visualisation, and quality control of reads
Event alignment
Hairpin analysis
Review of applications
Scaffolding of short reads
Hybrid de novo assembly

Covered software

BWA, Canu, DeepNano, GraphMap, HDF5 Command-line Tools, HDFView, IGV, Metrichor, LAST, LINKS, miniasm, minimap, minoTour, MUMmer, Nanocall, Nanocorr, nanopolish, poRe, pore tools, R, QUAST, SAMtools, SPAdes, SSPACE-LongRead