Simplex sequencing

Simplex, the standard nanopore technology mode, provides fast, high-output accuracy, suitable for most genomic investigations.

User experience of Simplex

Accurate variant calling and haplotype phasing

Simplex enables the generation of complete, reference-quality genome assemblies. Long and ultra-long nanopore sequencing reads (reads in excess of 4 Mb have been demonstrated) can span complex genomic regions, such as structural variants and repeats, which have proven challenging to assemble accurately using traditional short-read sequencing technologies. Long nanopore sequencing reads further enable haplotype phasing, supporting the assignment of sequencing data to maternally or paternally inherited chromosomes.

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Genome browser view of a human sample (NA02533) with Mucolipidosis type IV. Accuracy reported here has been calculated for 30x coverage, basecalling with the high accuracy model (HAC).

Customer experience of simplex

Nanopore has a reduced SNP error rate compared to [a short-read sequencing technology], especially in those low-mappability regions

Billingsley, K. London Calling presentation (2023)

Our work highlights the potential of the long-read sequencing in serving as a new platform for the precise diagnosis and treatment of [colorectal cancer].

Xu, L. et al. PLoS genetics, 19(2), e1010514 (2023)

We show that it is possible to achieve state-of-the-art small and structural calling performance using only ONT reads produced by a single flow cell at high throughput

Kolmogorov, M. et al., Nature methods, 20:10 (2023)

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Typical output over time of simplex data through a PromethION R10.1.4 Flow Cell using Kit 14 chemistry, at 5 kHz.

High-output technology

With simplex you can achieve up to 30x whole human genome coverage on a single PromethION Flow Cell for established workflows. Furthermore, nanopore sequencing can directly characterise base modifications (e.g. methylation) alongside the nucleotide sequence ― delivering richer biological insights, without additional sample processing or costs.

Discover our end-to-end protocols ― from sample and library preparation to data analysis ― for a range of applications.

See how simplex is being used by the Nanopore Community

Miten Jain: Human genome assembly and analysis using R10.4.1 and Kit 14

Miten Jain's team at University of California, Santa Cruz, USA assessed recent improvements in read length, accuracy, and software for ultra-rapid, nanopore-based whole-genome sequencing analysis. Focusing upon Kit 14, Miten presented data generated in the days immediately prior to this talk, showing the generation of over 140 Gb of sequencing data on a single PromethION Flow Cell. This high output is achieved with lower DNA and library input requirements than for previous nanopore sequencing chemistries. Also highlighted was a notable improvement in raw read accuracy, particularly evident in homopolymer regions where lengths of up to approximately 20 bases were accurately called.

Kimberly Billingsley’s team developed an efficient and scalable wet lab and computational pipeline for long nanopore sequencing reads. They applied their pipeline to ~300 human brain samples from the North American Brain Expression cohort and demonstrated that this data can be used to phase small and structural variants at megabase scales, better resolve disease-relevant haplotypes, and produce highly accurate haplotype-specific methylation calls. As part of the NIH Center for Alzheimer’s and Related Dementias (CARD) long-read sequencing initiative, they are currently applying this framework to thousands of human brain samples to generate a new long-read resource for the wider research community.

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