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Discovery Genomics

Discovery
Genomics

Delivering research genomics and data analysis at scale
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Do you accept samples from international researchers?

Yes we do. Our whole genome sequencing services are readily available worldwide.

What whole genome sequencing (WGS) services do you offer?

We offer WGS services using the protocols specified in the table below:

ProtocolTotal DNA RequiredApplicationsRead LengthPlatform
TruSeq Nano DNA Library Preparation Kit >1 ug Whole genomes of all species.
Insert size: 450 bp
2 x 150 bp Illumina HiSeq X Ten
KAPA Hyper PCR-Free Library Preparation Kit >1.2 ug Whole genomes of all species.
Insert size: 450 bp
2 x 150 bp Illumina HiSeq X Ten
Researcher Submitted Library for WGS 10 nM Whole genomes of all species Expected library size: 580 – 850 bp* 2 x 150 bp Illumina HiSeq X Ten
Chromium Genome Solution Library Preparation Kit >0.5 ug. Input gDNA with a mean length >50 Kb Whole genomes of all species 2 x 150 bp 10X Genomics Chromium Genome Solution + Illumina HiSeq X Ten
Researcher Submitted Chromium Library for WGS 10 nM Whole genomes of all species Expected library size: 580 – 850 bp* 2 x 150 bp Illumina HiSeq X Ten

* If libraries fall outside of these parameters, the researcher will be contacted for how they would like to proceed.
To assist in determining which protocol would best suit the needs of your project, please contact us.

What are the DNA sample requirements?

DNA should be extracted using Qiagen DNeasy / Tissue Extraction kits or equivalent and submitted in Qiagen Elution Buffer (EB), Illumina Resuspension Buffer (RSB) or similar (10mM Tris / 1mM EDTA). Samples must be pure, intact, of high molecular weight and free of contaminating nucleic acids. Samples cannot be derived from FFPE material, should not be modified prior to shipping (e.g. bisulphite conversion) and must not be amplified. Sample quantification must be completed using a fluorometric assay specific to dsDNA (e.g. Picogreen, Qubit BR assay) and meet the following specifications:

What is the online manifest?

Researchers are given access to an online electronic manifest into which several sample characteristics, required for the processing of the sample, must be entered. The manifest is pre-filled with a barcode corresponding to each FluidX 2D tube provided for your samples. The barcode provides a unique identification code for each submitted sample.

How do I submit my samples?

DNA must be aliquoted into the pre-allocated FluidX 2D barcoded tubes provided by Genome.One.  Samples sent in any other container will not be processed. Please ensure the sample details entered for each barcode in the manifest, match the sample aliquoted into the corresponding barcoded tube.  Please ensure that the barcoded tubes sit securely in the rack (if provided) and the lid is locked using the orange clips on the side of the rack. Please ensure the rack containing the barcoded tubes are packaged into an appropriately rigid shipping container.

If no rack is provided, prevent damage to your tubes in transit by ensuring the barcoded tubes are stored securely as follows:
- place the Primary Receptacle (FluidX 2D tube) into a Secondary Receptacle (tube rack, Falcon tube or BioBottle)
- place the Secondary Receptacle into a Tertiary Receptacle (padded outer packaging)
- package the Tertiary Receptacle into an appropriately rigid shipping container

Please affix the provided shipping label containing the manifest ID to the outside of the shipping container.  Samples can be shipped at ambient temperature or on dry ice.

How is data delivered?

Data will be delivered via DNAnexus, a cloud-based platform. Your data will be shipped with a detailed project summary report describing the yield and quality of sequence data for each sample. With your data, you will also find documentation that describes the file structure of your sequencing data and a project summary report. In accordance with Illumina’s specification for the HiSeq X, we guarantee yield ≥100Gb and Q30 ≥75% of bases.

Can I view data from a reference sample that has been sequenced on your HiSeq X Ten platform?

These data are from the Coriell Cell Repository NA12878 reference cell line, which has been extensively analysed by the Genome in a Bottle Consortium. The sequencing libraries were generated with Illumina’s TruSeq Nano V2.5 kit using the Hamilton Microlab STAR robotics platform, achieving >400bp inserts. Each library was sequenced on a single lane of an Illumina HiSeq X patterned flow cell, achieving over 130Gb of yield, with > 83% of bases with quality > Q30 in just 2.8 days. The four data sets are of similar quality, and are provided to allow you to assess the reproducibility of the technology. Each data set substantially surpasses the minimum coverage and quality guaranteed by Illumina and is indicative of the potential for the Illumina HiSeq X Ten sequencing system.

Each of the four datasets consists of raw paired-end data (fastq.gz files) and results obtained with the GATK DNAseq best practices pipeline run on each library independently with the recommended parameters for whole genome sequencing.

Download the data to your computer or server, using the links below.

Human Sample Data

Key Metrics

LibraryNA12878_V2.5_Robot_1NA12878_V2.5_Robot_2NA12878_V2.5_Robot_3NA12878_V2.5_Robot_4
Flowcell H7LH3CCXX H7KMTCCXX H7CYCCCXX H7CYCCCXX
Lane 5 6 1 2
Read length 151bp PE 151bp PE 151bp PE 151bp PE
Raw Read Pairs (PF) 439,013,514 510,726,469 464,350,208 479,861,658
Raw Yield (Gb) 131.704 153.218 139.305 143.958
% bases >=Q30 (R1/R2) 92.39/81.23 93.18/73.37 89.89/77.44 93.00/78.75
% bases >=Q30 (mean) 86.81 83.28 83.67 85.88
Alignment % 98.448 98.972 95.53 97.911
Duplication % 10.6 11.549 10.592 12.032
Coverage (mean) 34.8873 39.51173 35.69027 37.34294
Coverage (stdev) 10.52019 11.37284 10.24081 10.57043

What is VECTIS and can I see a demo?

VECTIS is an integrated genomics platform to house, query, filter and enable easy analysis of genome data from diverse cohorts of any size. Every whole genome sequenced contains around 5 million variants from the reference genome, is approximately 250 Gb in size, and requires 700 hours of processing on high-end computers. VECTIS was developed to suit the needs of diverse users including scientists, clinicians, bioinformaticians and patients. The VECTIS platform will enable increasingly complex queries to facilitate the discovery of new genotype-phenotype associations and scale to meet the increasing demands of large-scale genomics projects.

Please click here to view the VECTIS platform, which has been custom designed and adapted for the Sydney Genomics Collaborative's Medical Genome Reference Bank.

What are your payment options?

We have flexible payment options available. Please contact us to discuss further.

How do I request a quote?

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