Established over a decade ago, the GIS Next Generation Sequencing Platform has evolved to become the largest and most productive academic sequencing facility in Singapore. GIS’ team of scientists also developed the first protein-mediated interactome protocol, ChIA-PET. As an endpoint service to a wide range of applications that answer different biological questions, the sequencing platform is critical to the ability to generate data from whole genome sequencing to RNA-sequencing, ChIP-sequencing, exome sequencing and more.
With a fleet of Illumina HiSeq and PacBio sequencers, the platform generates massive amounts of data – up to 150 teraBytes or 200 gigabases per year. These include 400 million reads per flowcell, in as short as a one-day turnaround. This state-of the-art sequencing platform is constantly updating itself with the newest technologies, to maintain its top spot as a sequencing service in Singapore. Not only does the platform look to produce reliable sequencing data in a high throughput manner, it is also expanding its capabilities with new machines to produce longer reads and allow miniaturised sample preparations.
Besides housing the newest and most capable sequencers, the sequencing group also automates parts of the process with liquid handlers.
Oxford Nanopore Long read sequencing
The GIS Sequencing and Genotyping Platform is a certified service provider for Oxford Nanopore Technologies in Singapore. Oxford Nanopore offers medium throughput long-read sequencing modalities to complement the very high-throughput, Illumina short read sequencing method.
Long-read sequencing is a timely addition to our collective repertoire of tools to study nucleic acids in living beings. The ability to sequence longer, contiguous pieces of DNA or RNA (at least a few thousand base-pairs using Oxford Nanopore methods) allows us to improve characterization of the architecture of living genomes, and make the realm of structural variants, a major source of genetic diversity, accessible for detailed study. This improves upon the inability of shorter read sequencing to reliably discover and characterize structural variants as they are most likely to be able to cover the length of the entire structural variant.
One of the trade-offs of long-read sequencing is the comparatively high sequencing error rate (>10 percent). Such errors can be reduced with increasing sequencing depth and better methods in bioinformatics sequence analysis.
We offer the following technical services:
- Whole genome sequencing using a selection of Oxford Nanopore devices (MinION, GridION, and PromethION). This method is particularly useful in efforts to construct more complete reference genomes.
- Metagenome sequencing (environmental genome sequencing). Application of long-read sequencing could allow for the generation of multiple thousands of high contiguity genomes and reveal previously uncharacterized genetic diversity.
- Long read RNA sequencing.