Services

Research applications currently supported

Genome sequencing

Gridion researchFor genome (and metagenome) sequencing we use the standard LSK109 ligation library prep kit from Oxford Nanopore. Native molecules are sequenced, enabling long read-lengths and detection of DNA modifications. Users should submit >1.2 µg of high-molecular weight DNA (the more, the better). We can perform optional short-fragment depletion or DNA shearing in order to maximise read-length or overall output from a given run, respectively. Up to 96 x samples can be multiplexed on a single flow cell. Please contact us for advice on DNA extraction protocols and sample preparation.

Transcriptome sequencing

Users may elect for cDNA or RNA sequencing. Direct-RNA sequencing enables detection of RNA modifications, while direct-cDNA sequencing generates higher outputs from a given run. PCR-amplified cDNA can also be sequenced, for projects where limited starting materials is available. Users can submit their sample as total RNA, polyA-enriched RNA or pre-prepared cDNA. Required quantities will differ between projects. Up to 96 x cDNA samples can be multiplexed on a single flow cell but multiplexing is not currently supported for direct-RNA sequencing. Please contact us for advice on RNA extraction protocols and sample preparation.

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. While we do not currently offer target enrichment as a service, users can submit DNA that they have pre-enriched via either method for sequencing. Up to 96 x samples can be multiplexed on a single flow cell. Please contact us for advice on targeted enrichment strategies.

Data delivery

Raw nanopore data is written in .FAST5 format and base-called to generate sequencing reads in .FASTQ format. By default, data will be delivered in .FASTQ format, which is suitable for most popular analyses. Users can also request access to the raw .FAST5 files for their project, which are required for signal-level analyses such as detection of DNA/RNA modifications or for base-calling updates, but users should be aware that these files are very large (>1TB for a typical PromethION flow cell). Both data types will be securely stored at Garvan for 3 months and extended data storage can be optionally purchased. Data will be delivered via Garvan’s FileSender system.

Custom projects and bioinformatics analysis

We appreciate that not all projects fit within our standard specifications and will consider all requests for custom jobs to suit the user’s needs. Users requiring bioinformatics support for their nanopore sequencing projects should enquire about how our experienced team can help.

Contact us

For enquiries about nanopore sequencing please email: nanopore@garvan.org.au

For sample submission, please use the following shipping address:

Attn: Genomic Technologies Group 
Garvan Institute of Medical Research, Precinct Loading Dock
West Street (off Burton Street)
Darlinghurst NSW 2010
Australia