Nanopore metagenomics: from sample to analysis 2025

The goal of this course is to provide an overview of lab and in-field, real-time nanopore sequencing using the Oxford Nanopore Technologies (ONT) platform.  

This course will cover theory of experimental methods and sample collection, plus theory and hands-on experience of DNA extraction and library preparation.  

The second part of the course will cover data analysis and visualisation providing hands-on opportunities including the use of QC tools, EI’s MARTi software and tools for Metagenome Assembled Genomes (MAGs), all delivered via virtual machines. 

You will also have the opportunity to discuss and apply lessons to your own projects with EI’s experts and a representative from Oxford Nanopore Technologies during an optional Q&A session. 

What will I learn? 

• Advantages and disadvantages of different extraction protocols 
• Familiarity with different DNA QC and library construction methods 
• Hands-on techniques for preparing samples for nanopore sequencing 
• Familiarity with nanopore sequencing outputs 
• Common analysis tools for alignment, assembly and classification of nanopore data 
• Capabilities of nanopore’s epi2me cloud-based data analysis platform 
• Effective use of MARTi software for real-time data analysis for species identification and quantification 
• Tools for assembly of Metagenome Assembled Genomes (MAGs) 

Who is this training for? 

You should be in the early planning stages of a project, wanting to understand the different approaches to sample preparation and explore options for comprehensive and rapid data analysis.  

Course prerequisites 

Some basic level of experience with the command line is necessary if you wish to follow the hands-on sessions. You would need to be comfortable using the functions covered in the Software Carpentry lesson, The Unix Shell. We suggest you refresh your memory of these lessons if needed. The commands used will be provided throughout the hands-on session.