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A summer* of nanopore – are you up to date?

Tue 17th September 2019

#nanosummer

 

As we gear up for what's set to be a busy rest of 2019, with a China Nanopore Tech Tour just around the corner and the New York Community Meeting hot on its heels, we’re taking a moment to reflect on some amazing progress from the Nanopore Community over the last few months.

Reading list

A number of high impact publications landed recently — here are a few to whet your appetite — you can visit the resource centre for more:

  • How much of the human genome is complete? Karen Miga and team published the 1st human chromosome assembly with 0 gaps, since the Human Genome Project was completed 16 years ago in April 2003.
  • On the topic of human genomes, 11 were sequenced and assembled in just 9 days by Shafin et al., using one PromethION. The highly repetitive and polymorphic MHC region was spanned entirely in 1 contig using Canu and Wtdbg2 assembly tools.
  • Soren Karst and team published in pre-print their method for long amplicons with unique molecular identifiers, getting an error rate of 0.03% across the whole rRNA operon of 4.4 kb.
  • A nanopore-based 3-in-1/combined CLL screening test, developed by Burns et al., proved to be accurate, low-cost and rapid. The workflow provided all information required to characterise the CLL in 5 days using one MinION flow cell.
  • O’Grady and team demonstrated rapid characterisation of bacterial lower respiratory tract infections in 6 hours, achieving 100% specificity and sensitivity.
  • The first publication featuring Flongle showed fast, low-cost and accurate genotyping of human enteroviruses with >99.7% sequence identity, for less than $10 per sample.

You may also be interested to read this review from Nature Methods, exploring the work a variety of users of nanopore technology and the boundaries that are being broken in the Community.

Or perhaps you’d rather watch than read — in which case, here’s a webinar from Ghamdan Al-Eryani, based on his experiences in developing and implementing single-cell technologies to understand how the immune system works in cancer.

New flow cell records: MinION and PromethION

July saw a new in-field record for the highest throughput from a single MinION flow cell — a huge 43Gb. Soren Karst takes the crown, generating the 43Gb from ~5000 bp amplicons prepared with SQK-LSK109 and run on a single R9.4 flow cell, (costing $500-$900) for 2 x 48 hours. Now that R10 is out in the field we look forward to seeing more record breaking numbers soon…

Many users have been benefiting from adding a nuclease flush to their workflows, seeing increased throughput from flow cells as a result. We’re launching a new Wash Kit this week which provides everything you need to carry out nuclease flushes – keep an eye out in the store!

Meanwhile, GrandOmics obtained over 180Gb from a single PromethION flow cell – that’s a long-read human genome at around 60X depth, including methylation information, for $500-$1700.

This was generated on the PromethION 48, which is now being shipped, and can generate over 7Tb in 72 hours. At 100Gb per PromethION flow cell, that is the equivalent of 50 human genomes to 30X coverage in just 3 days sequencing time.

Some updates from nanopore HQ

In July our new high-tech manufacturing facility — the MinION Building — came online to bring new, highly automated production process to the manufacturing of flow cells. Full, end-to-end production will be phased in over the coming months and the factory will support a significantly increased production capability, that will be able to exceed 1 million flow cells per year in 4-5 years.

At the end of the month we introduced the GridION MK1, which demonstrates a boost in GridION X5 performance at no additional cost. The GridION Mk1 contains cutting-edge GPU technology in the form of the Nvidia Volta GV100 card which provides an order of magnitude performance improvement on that in the GridION X5. This means that basecalling requires just 10% of GPU resource, leaving 90% available for additional analysis.

In basecalling news, Guppy upgrades mean you now get 5mC CpG methylation, dcm methylation and dam methylation, as standard, for free. It’s also possible to train for other modifications. Have you got the latest version?

Come and meet us!

If you aren’t in touch with us through the Community, we’d love to see you at one of our events. In September we’ll be hosting the first Nanopore Tech Tour in Beijing and Shanghai. We’re joined by an excellent line-up of speakers and have an agenda of live demos, tutorials and practical sessions planned. It’s sure to be a hugely insightful couple of days and we’re looking forward to hearing about the latest nanopore research taking place in the region.

October will see a team of nanopore experts land at booth #1127 at ASHG 2019. They’ll be there to hear about your research and provide insight as to how nanopore technology could fit with your work. We’ll also be hosting a seminar and an evening event — you can register here to join us.

This year’s Nanopore Community Meeting takes place in New York on 5-6th December. You can find the preliminary agenda here and we’ll be announcing speakers regularly between now and December. Register before 27th September to get a limited price ticket.

Want to find out more about nanopore sequencing?

Our Nanopore Days are free to attend and provide the opportunity to hear about the latest technology updates, and from local users about their work. You can also register to attend a training workshop. These provide a hands-on introduction to nanopore sequencing and data analysis.

*We’d love to hear about your highlights from the last few months, tell us about your #nanosummer (or #nanoseason, depending where you are in the world) on Twitter.

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