Our mission is to ensure the generation of accurate and precise findings.

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Work With The Experts

We offer a complete genotyping-by-sequencing (GBS) service — processing client supplied DNA into SNP markers. We work very closely with our clients from first contact to project completion — developing a collaborative relationship. When you bring your research to The Elshire Group, you work directly with genotyping-by-sequencing (GBS) experts and can leverage their deep knowledge with ease. We consider every project with care. This is a better way to do science.

Please note that we do not take any projects on human or CITES listed species.

We only accept extracted DNA. It is not possible for us to import tissue due to the nature of the New Zealand biosecurity system.

Genotyping-by-Sequencing Service

Project Setup & Consultation

Because genotyping-by-sequencing can be applied to many different species and research questions, we work directly with our clients to provide a customised project plan. This process starts with an email to us. See our contact us page for details.

Species / Enzyme Combination Optimisation or Validation

This step is necessary for each species / enzyme combination that we have not done before in house. It is necessary to have the right ratio of adapter molecules to sample DNA fragments to generate a quality genotypings-by-sequencing library. This step is a minor part of the process in terms of time and cost, but important for success.

Genotyping-by-Sequencing (GBS) Library Preparation

Our standard laboratory method differs from the original genotyping-by-sequencing (GBS) method in that we use combinatorial barcodes and paired end sequencing. We provide our clients with clear instructions for all steps of the process. Below, we provide information on the enzymes and multiplexing levels that we offer. If you require something different, please let us
know and we will look at the options together.

Enzymes

  • ApeKI

  • PstI

  • NsiI (an isoschizomer of EcoT22I which is no longer available)

Multiplexing

Multiplexing is the number of same species samples that are put together into one library. We offer a number of levels of multiplexing. Our most popular are 94 plex and 188 plex.

DNA Sequencing

DNA sequencing is performed on an Illumina NovaSeq with 2 x 150bp paired end reads. Typical yields are 300 to 400 million read pairs per lane of sequencing (over 800 million total reads). This equates to an average of 3.7 million read pairs per sample for a 94 plex or 1.8 million read pairs per sample for a 188 plex.

SNP Calling

Currently, we provide SNP calling using either the reference based SNP calling pipeline in TASSEL 5 GBSV2, the denovo SNP calling pipeline TASSEL-UNEAK, or discoSNPRad.

Timing

We typically are able to provide you with a quote within 4 working days. We provide our services on a first come first served basis, unless otherwise agreed. Turn around time is dependent on our work queue. Please inquire to find out the current status of the queue.

Collaborating with us

Students

We regularly engage with graduate students in our projects, enjoying the opportunity to support their training. Our extensive experience ensures we can effectively guide students, from start to finish, with their genotyping-by-sequencing (GBS) research components.

Laboratory Staff

To generate superior genotyping-by-sequencing (GBS) data, high-quality DNA is a must. We engage directly with wet lab researchers, providing clear protocols and rapid answers to any questions, so they can work confidently.

Bioinformaticians

Some collaborators choose to take on the SNP calling themselves after we complete the library prep and DNA sequencing. Our experience shows that genomics experiments yield better results when a bioinformatician is involved from the beginning. We recommend clients create an analysis plan upfront. We provide detailed information on the sequencing procedures used and the data that is generated.

Additional Services

While we focus on providing an expert genotyping-by-sequencing (GBS) service, we are passionate scientists with a range of interests and expertise. From time to time we consider picking up other interesting work. If there are other types of projects that you would like collaborate with us on, please check out our individual team pages and contact us.