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Nanopore sequencing

Providing Australia’s leading Oxford Nanopore sequencing services to the local and international scientific community

The Garvan Sequencing Platform operates Australia’s leading Oxford Nanopore research sequencing service. Nanopore technology enables sequencing of long, native DNA/RNA molecules, with no theoretical upper limit on read-length. Common research applications for nanopore sequencing include:

  • Genome sequencing and assembly
  • Resolving challenging genomic features, such as repetitive regions and structural variation
  • Characterisation of full-length RNA isoforms and alternative splicing
  • Detection of DNA/RNA base modifications, such as 5-methylcytosine (5mC) and N6-Methyladenosine (m6A)
  • Metagenomics and pathogen sequencing.

We offer genome, transcriptome and metagenome sequencing projects of any size or specifications and pride ourselves on supporting custom research projects that push the boundaries. Our services are available to Garvan researchers and the broader scientific community, on a fee-for-service basis.

Genome sequencing

  • For genome (and metagenome) sequencing, we use the latest ligation library prep kit available from Oxford Nanopore. Native molecules are sequenced, enabling long read-lengths and detection of DNA modifications.
  • Input DNA can be sheared to the researcher’s desired specifications and ultra-long read sequencing (>80 kb reads) is supported.
  • Up to 96 x samples can be multiplexed on a single flow cell.
  • for advice on DNA extraction and sample preparation.

Transcriptome sequencing

  • We offer sequencing of cDNA or RNA directly. cDNA sequencing will generate higher output, whereas direct-RNA sequencing enables detection of native RNA modifications.
  • A PCR-amplified cDNA sequencing prep is also available, where starting material is limited.
  • Researchers can submit their sample as total RNA, polyA-enriched RNA or pre-prepared cDNA.
  • Up to 96 x cDNA samples can be multiplexed on a single flow cell. Sample multiplexing is not currently supported for direct-RNA sequencing.
  • for advice on RNA extraction and sample preparation.

Single-cell and spatial sequencing

  • We work closely with Garvan's Cellular Genomics Platform to enable single-cell or spatially-resolved long-read transcript sequencing.
  • Nanopore long-read sequencing is compatible with standard 10X and Visium cell capture and barcoding systems.

Targeted sequencing

  • Targeted sequencing of specific transcripts, gene loci or viral genomes can be achieved by PCR amplification or hybrid-capture, followed by nanopore sequencing.
  • We do not currently offer target enrichment as a service, but researchers can submit pre-enriched DNA via any of these methods.

Programmable targeted sequencing with ‘ReadUntil’

  • The ‘ReadUntil’ application enables programmable selective sequencing on genomic DNA.
  • This can be used for targeted profiling of virtually any gene or target region within the human genome.
  • Please enquire about the suitability of ‘ReadUntil’ sequencing for your projects.

Custom projects

We appreciate that not all projects fit within our standard specifications and will consider all requests for custom jobs to suit a researcher’s needs.

The PromethION P48 is the largest instrument from Oxford Nanopore and enables comprehensive sequencing of large Eukaryotic genomes/transcriptomes.

  • A single PromethION flow cell has 3,000 nanopore channels, providing up to 12,000 pores for sequencing.
  • 50X human genome coverage).
  • Sequencing outputs vary significantly, depending on sample quality, fragment sizes and other sample-specific variables. Please contact us for recommendations.

The smaller MinION device from Oxford Nanopore may be used for custom projects where the PromethION is unsuitable, but MinION sequencing is not offered as part of our standard service.

Nanopore services are offered by the Garvan Institute of Medical Research’s Sequencing Platform. The platform provides local and international customers with access to scalable DNA sequencing and expert genomic analysis. If you would like to access our nanopore sequencing services, please contact us at: nanopore@garvan.org.au.

Our turnaround timeframe ranges from two to six weeks. Faster turnaround times can be arranged under special circumstances. In the event that any samples or projects don’t meet agreed QC metrics, customers will be notified to seek an agreement on whether/how to proceed.

Submitting your samples

Please consult our team to determine the required specifications before submitting your sample.

Please send samples via mail or courier to: 

Attention: Genomic Technologies Group  

Garvan Institute of Medical Research  

Precinct Loading Dock 

West Street (off Burton Street)  

Darlinghurst NSW 2010  

Australia 

Phone: +61 (0) 2 9355 5883 

Please share your tracking number at the time of shipping as this will allow us to monitor your shipment. We will notify you when your samples have been received.

For international customers 

Your samples must be accompanied by relevant documentation in order to enter Australia. Please consult our team about these requirements before shipping your samples. We currently recommend World Courier, LabCabs, DGI and Logical Freight Solutions. We advise against the use of DHL or FedEx for international shipment of precious samples to Australia. 

Data processing and delivery

We provide raw nanopore signal data in SLOW5 format and base-called reads in FASTQ format.

  • Base-calling is performed using ONT’s Guppy software with the ‘high-accuracy’ model.
  • ‘Super-accuracy’ base-calling can be requested at additional cost.
  • Data is delivered through Garvan’s FileSender server and is securely stored on-site for up to three months. Extended data storage can be purchased if required.