The Oxford Nanopore (ONT) sequencing platform is capable of generating ultra-long reads that are only limited by the size of the nucleic acid extracted (in excess of 1 million nt). Using this device, single DNA (or RNA) molecules are sequenced without the need for PCR amplification of the sample, enabling sequencing of native structures and modifications. We recommend using this platform when leveraging the long read length or direct, PCR free, sequencing capabilities of this instrument is integral to your research project. 

We provide full-service support for all ONT library preps. We maintain inventory of the Ligation Sequencing Kit V14 (LSK114) and PromethION R10 flowcells for DNA sequencing applications. Although we fully support other ONT assays, we do not regularly keep stock of alternative kits and flowcells. Therefore, advanced planning and consultation are necessary for alternative assays, and reagent costs are not included in our service pricing.

We currently specialize in sequencing high molecular weight genomic DNA (HMW gDNA) for genome assembly projects. Obtaining a pure HMW gDNA sample is critical to maximizing sequencing output and quality, because sequencing yields are typically lower for HMW gDNA. If you are considering using this platform for genome assembly, please set up a consultation to discuss your project.

Instruments and Flowcells

• PromethION: Each PromethION flowcell contains 10,700 pores and typical outputs range from 25-100Gbp depending on sample type and quality. The cost per read is lowest for PromethION flowcells.
• MinION: Each MinION flowcell contains 2,048 pores and typical outputs range from 5-15Gbp of data depending on sample type and quality.

Prior to initiating an ONT project, we recommend a preliminary sample QC check (Femto QC for HMW gDNA, or standard QC for DNA/RNA samples). Based on the observed DNA size distribution, we offer an optional service for ‘‘short fragment elimination’ for HMW gDNA samples before initiating library preparation.

ONT services include library preparation (optional multiplexing allows multiple samples to be pooled for sequencing on one flowcell), sequencing on the ONT flowcell (multiple reloads are typical to maximize data generation), and real-time high-accuracy base calling (HAC). Super accuracy basecalling and detection of modified bases is not included in our service due to real-time limitations. We recommend that POD5 data files be re-analyzed on the BioHPC system available via the Bioinformatics Facility (or other high performance compute resources) to improve basecalling accuracy and to leverage the best models for detection of modified bases.