PromethION Sequencer

The first high-throughput third-generation sequencer in New Zealand

Bragato Research Institute has installed an Oxford Nanopore PromethION Sequencer at their new Grapevine Improvement Laboratory at Lincoln University to support research in grapevine improvement and other fields. This capacity is also available as a service to other research agencies and customers.

PromethION offers increased throughput and reduced cost-per-gigabase for long-read sequencing of DNA and RNA samples. BRI’s model (PromethION 24 A100) can generate up to 100 gigabases of sequence data per flow cell (depending on samples and library types), and can simultaneously run up to 24 flow cells.

Nanopore sequencing

Nanopore sequencing works by passing molecules of DNA or RNA through tiny pores in a membrane and measuring changes in the electrical current flowing through the pores.

This allows much longer molecules to be read (up to a million bases and above), enabling complex parts of genomes and transcriptomes to be studied. The sequence data is generated in real time and base modifications, which can play a role in regulating gene expression, can be included.

More information on how the PromethION Sequencer works can be found at the Oxford Nanopore Technology website by clicking here.

Bragato Research Institute has installed the PromethION 24 A100 model

Key features

• Capable of running up to 24 independent flow cells concurrently, generating up to 7 terabases (7 x 1012 bases) of sequence data from multiple sample types.

• Samples can be combined on a single flow cell by indexing.

• Onboard GPU-based hardware for live base calling.

• Fully supports new high-accuracy Q20+ sequencing protocols.

• High-speed data delivery via the REANNZ network.

Applications

PromethION sequencing is suited to a wide variety of project types, including:

• Chromosome-level genome assembly

• Epigenetic base modifications of DNA / RNA

• Transcriptomic experiments, including isoform analysis

• Metagenome sequencing – complete genomes from mixed samples

• Targeted sequencing in real time (adaptive sampling)

• Population-scale genetic surveys

Data delivery

• BRI supplies raw nanopore data in .FAST5 This data is transferred to NeSI, where it is stored for 30 days on the clients account. Clients should be aware that these files are very large (>1TB data for a typical PromethION flow cell).

• Data is then base-called to generate sequencing reads in .FASTQ format, which is suitable for most popular analyses.