Leverage Our Experience and Innovation

Faster computer processors and advanced sequencing technologies are expanding whole genome sequencing to large-scale studies, including clinical research and decision-making. But achieving the required speeds and throughputs can be challenging for many genomic service labs.

At HudsonAlpha Discovery, we have the infrastructure and expertise to quickly and successfully reach your study goals, whether you’re embarking on an on-going, large-scale clinical whole genome sequencing study or have a one-time need to support basic research.


Delivering scalable whole genome sequencing services with the coverage options and quality to meet your project needs.


Flexible and customizable end-to-end services


A PacBio Center of 


Short- and long-read 
NGS capabilities


Capacity to sequence 
70,000 human 
genomes per year


  • Genomic variant and biomarker analysis
    •  Single nucleotide variants (SNV)
    •  Insertions and deletions (InDels)
    •  Copy number variation (CNV)
    •  Tumor Mutation Burden (TMB)
    •  Additional analyses—ask us to learn more
  • Long-read PacBio and Oxford Nanopore options including de novo genome assembly
  • Disease research
  • Biomarker discovery
  • Personalized medicine
  • All research phases and activities
    •  Basic discovery
    •  Translational and pre-clinical
    •  Clinical

Whether you need end-to-end support or a subset of what we can provide, we’ll help you customize a service project to best meet your study objectives.

Highlights of Our Whole Genome Sequencing Service

Here are a few examples of what we offer:

Nucleic Acid Extraction and Library Preparation

  • Optimized extraction protocols for nearly any sample type
  • Optimized protocols for working with ultra-low amounts of nucleic acid
  • Dual concurrent RNA-DNA extraction from challenging sample types such as FFPE tissue—read the white paper

Sequencing Depth

  • 30x coverage for germline and normal WGS
  • 60x, 90x coverage for somatic variant detection in oncology or other high-coverage applications
  • Custom

Read Length

  • Standard: Dual-index 150 base paired-end reads on Illumina instruments
  • Long-read: PacBio or Oxford Nanopore
  • Combined short- and long-read platforms

    Illumina short-reads for high quality base calling, SNV, InDel, and CNV accuracy

    PacBio and Oxford Nanopore for scaffolding difficult-to-read portions of the genome, detection of large structural variants (e.g., inversions, translocations, large InDels, etc.) and de novo assembly of unique genomes.

Bioinformatics Analysis and Data Storage

  • Tier 1: Raw BCL and FASTQ file output
  • Tier 2: Standard application-specific and quality report outputs (BCL, FASTQ, aligned BAM files and sequencing QC reports
  • Tier 3: Standard output plus variant calling (VCF, g-VCF) and genomic interpretation reports
  • Additional custom reporting options including Ingenuity Variant Analysis (Qiagen) consolidated variant reports as well as options for genomic variant annotation
  • Flexible data delivery and storage options
  • 90 days storage included with service pricing
  • Long term storage available

Whole genome Sequencing

The HudsonAlpha Discovery Difference

Flexible and creative problem solving with expert scientific guidance


Optimized protocols and automated workflows that reduce technical bias


Stringent quality control parameters—we consistently exceed manufacturer specifications—for reproducible, accurate results


Massive scale with 9 Illumina NovaSeq 6000 sequencers as well as NextSeqs, MiSeqs, and iSeqs


A decade of proven experience spanning thousands of projects and hundreds of publications


Leverage the power of the HudsonAlpha Discovery division:


Featured Paper

Whole Genome Sequencing for Prognosis

Applying whole-genome sequencing in relation to phenotype and outcomes in siblings with cystic fibrosis

Wilk MA, et al. Cold Spring Harb Mol Case Stud. 2020 Feb 3;6(1):a004531. PMCID: PMC6996517.

In this study, completed when the HudsonAlpha Discovery lab was still the HudsonAlpha Institute Genomic Services Lab, our whole genome sequencing services were used to sequence the whole genomes of three siblings with cystic fibrosis. The goal of the study was to identify genomic variation associated with the severity of the disease.

Their findings: “Our data show that there is notable genomic variation in CF related loci across these three siblings with CF.”1

Their findings: “To our knowledge, this is the first application of WGS to individual patients with CF applied in an effort to clarify (and eventually predict) the course of the disease in a strategy of personalized/precision medicine.”1

Recent Publications

  1. Wilk MA, et al. Applying whole-genome sequencing in relation to phenotype and outcomes in siblings with cystic fibrosis. Cold Spring Harb Mol Case Stud. 2020 Feb 3;6(1):a004531. PMCID: PMC6996517.
  2. Cochran JN, et al. Genome sequencing for early-onset or atypical dementia: high diagnostic yield and frequent observation of multiple contributory alleles. Cold Spring Harb Mol Case Stud. 2019 Dec; 5(6): a003491. PMCID: PMC6913143.
  3. Mead ME, et al. Draft Genome Sequence of the Griseofulvin-Producing Fungus Xylaria flabelliformis Strain G536. Microbiol Resour Announc. 2019 Sep; 8(38): e00890-19. PMCID: PMC6753274.
  4. Ma X, et al. Analysis of Error Profiles in Deep Next-Generation Sequencing Data. Genome Biol. 2019 Mar 14;20(1):50. PMCID: PMC6417284.

To propel your projects with The Power of Discovery.™

Contact Us Today

Let us know about your project!