London Calling 2024 opens with a day of masterclasses delivering everything you need to know for sample-to-answer nanopore sequencing
Kicking off the masterclass series this year was Akelia Wauchope-Odumbo (Associate Director, Technical Applications — Americas) with How to get started with nanopore sequencing and plan your experiment. With the ability to directly sequence DNA and RNA over five magnitudes in length and detect genomic variants and native base modifications in a single run, Akelia highlighted how nanopore sequencing generates ultra-rich data, revealing more biology. Introducing everything needed to get started with nanopore sequencing, Akeila provided an overview of the nanopore workflow — from experimental planning right through to data analysis.
Providing the first deep dive into the nanopore sequencing workflow, Vânia Costa (Applications Scientist) shared expert advice on How to extract high-quality DNA and RNA from a wide range of samples. With her motto ‘you cannot sequence what you do not have’, Vânia showed us how to optimise extraction to meet our experimental goals. Summarising a wealth of information in an example, Vânia guided us through how to extract DNA from a human cell line when investigating genomic and epigenomic variation.
Then, taking us from extracted samples to nanopore sequencing libraries was Jess Anderson (Senior Field Applications Scientist) who shared her expertise on How to select the right library prep workflow for your experiment. With nanopore sequencing kits available to suit every experiment, Jess described PCR-free DNA and RNA library prep methods — enabling direct analysis of epigenetic modifications with no additional sample prep — and PCR-based options for those with low sample input. Jess also described multiplexing options and targeted sequencing methods, including adaptive sampling: an on-device, PCR-free enrichment method.
Next, it was time to sequence those libraries, and Tomek Dobrzycki (Field Applications Scientist, New Product Introduction) shared How to load a PromethION Flow Cell in an interactive demo. To first get us familiar with the equipment, he provided a detailed run through of how to load a flow cell on a PromethION 2 Integrated, and then — ‘for the moment you've all been waiting for’ — led us through the process step by step, so we could follow along with demo kits and see how quick and simple it is to load a PromethION Flow Cell ourselves.
After Tomek kicked off a sequencing run on the PromethION 2 Integrated, it was over to Bryant Catano (Senior Product Support Scientist) to show us How to run your sequencing device and get started with data analysis. Bryant took us through how to use the sequencing software MinKNOW, including how it converts raw data into basecalls. He also gave a demonstration of how to set up a sequencing run in MinKNOW and finished with tips on how to monitor a nanopore sequencing experiment in real time.
Following on from Bryant’s introduction to data analysis was Jimmy Creith (Field Applications Scientist, Bioinformatics), who walked us through How to analyse your data with EPI2ME — an intuitive data analysis interface for all levels of bioinformatics experience. Jimmy described the many preconfigured workflows available in EPI2ME for the final step in this sample-to-answer journey, from the comprehensive analysis of genomic and epigenomic variants with the human variation workflow, to metagenomic or 16S analysis and further infectious disease research workflows.
Last but not least, this year’s masterclass series finished off with a sample-to-answer deep dive into the nanopore-only microbial isolate sequencing solution (NO-MISS) in How to sequence microbial isolates with the NO-MISS workflow. Alex Trotter (Development Scientist – Translational Development) highlighted how, unlike legacy short-read technologies, the use of nanopore-only data produces complete, high-quality microbial genome assemblies, resolves plasmids, and enables characterisation of antimicrobial resistance (AMR) genes and their locations. Alex took us from choosing the right extraction method for different isolates, to library preparation with the Rapid Barcoding Kit, to scalable, on-demand sequencing on MinION or GridION. Finally, it was over to Chris Alder (Bioinformatician), who showed how this sequencing data can be analysed using the isolates mode of the EPI2ME workflow wf-bacterial-genomes, outputting a report covering multi-locus sequence typing, AMR, and serotyping for Salmonella research samples.
Find out more about NO-MISS in the bacterial isolate sequencing workflow.
Missed the masterclass series today? Head to the online London Calling platform to watch them on demand. The full series will also be available in the Resource Centre from the 3rd June.