OXFORD, OXFORDSHIRE, UNITED KINGDOM, December 3, 2020 /EINPresswire.com/ — Advances are announced as part of broad technology update at the Nanopore Community meeting
During an update at the 2020 Nanopore Community Meeting, Oxford Nanopore revealed a number of key advances in its sequencing technology. These include the release of new improvements in PromethION flow cells that have enabled a new 10 Terabase sequencing record, modal single-read accuracy of 99.1% using a new sequencing chemistry currently in development, high accuracy variant calling tools and automation options for nanopore sequencing experiments at any scale.
Further accuracy improvements
A new analysis algorithm, Bonito CRF, was recently released by Oxford Nanopore, that provides increased accuracy single read basecalling – the process of identifying the sequence of bases on an individual molecule of DNA. This latest update to Bonito builds on previous work to deliver improved performance, and is trained with a larger, more diverse data set. Using Bonito CRF, Oxford Nanopore has shown 98.3% single read accuracy on the current chemistry, and nanopore customers have also reported >98% single read accuracy.
High single read accuracy supports very high consensus accuracy (where a molecule is sequenced multiple times); optimised analysis tools including Guppy/Bonito basecalling, assembly with Canu/Flye and polishing with Medaka, can now enable Q45 with R9.4.1 flow cells and Q50 with R10.3 flow cells.
Variant calling performance is also improving with the latest releases; structural variation (SV) accuracy has reached gold standard of 96% with 30X rather than 60X coverage. SNP accuracy is now at 99.92%, which is comparable to short read accuracy.
In addition, this week Oxford Nanopore has generated modal raw-read accuracy of 99.1% (99%=Q20) using a new chemistry with Bonito, delivered on internal validation sets with a substantial fraction of these raw reads above Q20.
A new yield record
In November, Oxford Nanopore started to ship PromethION flow cells that incorporated a number of iterative improvements in yields and consistency. These improvements have culminated in a 10 Tb internal run using all 48 Flow Cells, a 25% improvement on the previous record. The median output per Flow Cell in this run was 208 Gb — the equivalent of two human genomes over 30X coverage. This success has been reflected in customer data, with increasing yields reported across a range of applications.
Further improvements on the PromethION platform are expected with the release of R10.3 PromethION flow cells in the coming weeks.
Automated sample preparation, at scale
As the number of users of nanopore sequencing in production-scale environments increases, Oxford Nanopore has been focusing during 2020 on automation solutions that enable users to run high numbers of samples, to run larger projects, or simply to automate everyday workflows.
Oxford Nanopore is collaborating with Hamilton to combine expertise to automate library preparation workflows on Hamilton’s NGS STAR 96. The first protocol released through the collaboration enables preparation of 96 samples in under 5 hours, with only one hour of hands-on time. One run fills two PromethION 48s, enabling high yield, highly validated sample prep and sequencing output.
Oxford Nanopore is also working with Opentrons to deliver mid-range lab automation that is suitable for users running the MinION or GridION devices. Opentrons automation liquid handlers are accessible, compact, and can support 2,500 LamPORE tests a day or automation of the Ligation kit, and ARTIC native barcoding method, as well as being suitable for future PCR based applications.
On the small scale level VolTRAX has seen a number of developments this year, including the development of a PCR-ready cartridge design which will be available soon, alongside the existing Sequencing and Multiplex Kits.
Oxford Nanopore Technologies
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Source: EIN Presswire