Oxford Nanopore's annual London Calling conference starts with a day of virtual masterclasses

This year’s London Calling conference got off to a busy start, with seven masterclasses walking the virtual audience through everything they need to know to perform their nanopore sequencing experiments. Oxford Nanopore sequencing experts delivered sample-to-answer training, with topics spanning from sample preparation, to sequencing and finally data analysis. The online attendees also had the option to learn from a breadth of content on the virtual platform from posters, to pre-recorded Mini Theatre presentations and product information in the Live Lounge.

Here's a quick overview of the masterclass sessions, all of which will be available to watch online on our website from next week.

Introduction: Getting started with nanopore sequencing & planning your experiment

Concetta Dipace, Technical Services Manager, kicked off the masterclass series with a session explaining how nanopore sequencing works and the key benefits and features of nanopore sequencing technology. She then outlined how to plan a nanopore sequencing experiment and what to expect when setting up the first nanopore sequencing run.

Preparation: Extracting high-quality DNA and RNA

Next, Vânia Costa, Applications Scientist, moved on to the first stage of the experimental workflow: extraction. She delivered expert advice on extracting high-quality DNA and RNA from a wide range of samples and how to check their quality. This was followed by best practices for storing and handling extracted nucleic acids, including the impact of freeze/thaw cycles and storage conditions. She finished by sharing extraction guidance for two cancer research-focused examples: extracting DNA from FFPE samples and extracting cell-free DNA (cfDNA).

Preparation: Selecting the right library prep method for your experiment

Covering the next stage of preparing samples for sequencing, Tomek Dobrzycki, Technical Applications Scientist, delivered his masterclass on choosing a library preparation method that would best suit your experimental goals. He discussed the different library preparation options available for the nanopore sequencing of DNA, RNA, and cDNA, as well as the difference between rapid and ligation chemistry. Finally, Tomek went through the applications and benefits of different sequencing techniques, including targeted approaches with PCR-based and PCR-free options.

Sequencing: Choosing the right nanopore sequencing device for you

Moving on to sequencing, we then had a chance to hear from Bryant Catano, Technical Applications Scientist, about the range of nanopore sequencing devices available and which devices best suit different experimental goals. Bryant began by describing the different flow cell types available – MinION, PromethION, and Flongle – and the throughputs possible with each, before introducing how each flow cell type is paired with different nanopore sequencing devices and how they suit different sequencing requirements. This was a great overview of the nanopore sequencing range, from portable to benchtop, and their unique benefits.

Sequencing: Loading a Flongle Flow Cell

After the success of this virtual session last year, viewers were again given the opportunity to get hands-on, with the interactive Flongle Flow Cell loading demonstration. Those users who had pre-registered for the demonstration received everything required to follow along with Andrada Tomoni, a Development Scientist at Oxford Nanopore. In the first half of the presentation Andrada introduced the components of the Flongle Flow Cell, before demonstrating the prime, flush and load steps as they would be carried out in the lab. For comparison, she then showed the similarities and differences of these same steps when using MinION and PromethION Flow Cells. With that covered, it was time for viewers to have a go at loading a Flongle Flow Cell themselves.

Analysis: Basecalling your data and detecting methylation

Following on from preparation and sequencing, it was then time to move to data analysis. Jessica Anderson, Technical Application Scientist, gave her masterclass on how to basecall nanopore sequencing data, how to choose the right basecalling model, and how to call methylation in the data. This started with the basics of nanopore sequencing data analysis, including the different approaches available and file types involved, before moving on to the basecalling options available, and how to choose a basecalling model to suit the specifics of an experiment. Finally, Jessica outlined how to call methylation from PCR-free nanopore sequencing datasets, therefore detecting methylation directly from native DNA and RNA sequencing data.

Analysis: Generating assemblies and calling variants

In the final masterclass of the day, Anthony Doran, Senior Technical Applications Scientist, talked through the approaches available for assembling nanopore sequencing data and calling variants, including single nucleotide variants (SNVs) and structural variants. This involved an overview of the different approaches for assembling nanopore sequence data across a range of experiments – from assembling a human genome to metagenomic assembly – and an introduction to the different file formats involved in nanopore sequencing data analysis and the workflows for calling variants, including structural variants and SNVs.

This year’s conference is, for the first time, a hybrid event and you can still register for online attendance for the live presentations over the next two days here: https://nanoporetech.com/lc22