Low-Pass Whole Genome Sequencing

Low-pass whole genome sequencing (also referred to as LP-WGS or shallow whole genome sequencing) is an inexpensive, high-throughput, DNA-sequencing technology used to accurately detect genetic variation within the genomes of a multitude of species. In addition to being an inexpensive alternative to genotyping arrays, LP-WGS enables the discovery of new rare variants with higher statistical power and provides an order of magnitude more data. From complex-trait association studies to calculation of genome-wide polygenic risk scores, low-pass whole genome sequencing can be used in multiple ways to address questions involving statistical and population genetics.


What is low-pass whole genome sequencing?

Low-pass whole genome sequencing is a technique in which each base in the entire genome is sequenced a few times (known as low-depth coverage). On average, the depth of coverage is below 5 times and can be as low as 0.1-1 times.

By reducing the depth of coverage, the cost of sequencing the whole genome is reduced while maintaining a broad look at the full genome.

What is imputation in low-pass genome sequencing?

Imputation is the generation of sequencing data in parallel to reference data. In low-pass whole genome sequencing, imputation is important in accurately associating and evaluating genetic markers that are not directly sequenced.

LP-WGS relies on computational methods, called imputation, to fill in the missing information. Imputation algorithms allow up to 99% accurate variant call detection as compared to genotyping arrays. The unique combination of Azenta Life Sciences, formerly GENEWIZ’s LP-WGS and imputation enables scientists to efficiently obtain analysis-ready fully-imputed VCF files in a single service. For applications that require deep sequencing coverage of specific genomic regions or variants (i.e. clinical applications), Azenta‘s LP-WGS Plus combines LP-WGS with exome or targeted sequencing - the first of its kind on the market.

Low-Pass Whole Genome Sequencing Workflow

  • 1. Experimental

  • 2. Sample

  • 3. Extraction

  • 4. Library

  • 5. Sequencing
    0.1x -<10x

  • 6. Imputation

  • 7. Variant


† WES coverage is limited to genic/exonic regions; hence, structural variants and copy number variants present only in these regions can be resolved.


Standard Deliverables

  • Sample QC (includes raw data QC & alignment metrics)
  • FASTQ files
  • Aligned BAM file
  • Imputed VCF file

Human LP-WGS Deliverables
(In addition to standard deliverables)

  • Copy number variant analysis
  • Ancestry analysis
  • Calculated polygenic risk scores files

Custom bioinformatics analysis and reports are available. Please contact us about how we can customize the analysis to answer your biological question.


Azenta’s LP-WGS Plus combines LP-WGS with exome or targeted sequencing – the first of its kind on the market.


  • Superior Data Quality
    Exceeding manufacturer’s benchmarks​

  • Real-Time Project Updates
    Through our online system

  • Ph.D.-Level Support
    At every step

  • Highly accurate variant calls across the genome

  • 10x more data than microarrays at 1/10th of the cost of standard WGS

  • High-throughput, cost-efficient and scalable

  • Low-Pass WGS Plus is a cost-effective solution for applications that require deep sequencing coverage of specific genomic regions or variants

    Low-pass sequencing increases the power of GWAS and decreases measurement error of polygenic risk scores compared to genotyping arrays

    Learn how low-pass sequencing plus imputation, in addition to providing a substantial increase in statistical power for genome wide association studies, provides increased accuracy for polygenic risk prediction at effective coverages of ∼ 0.5x and higher.

    Low-coverage sequencing cost-effectively detects known and novel variation in underrepresented population

    In this study, scientists from around the world (led by a group at the Broad Institute) considered specifically the question of association studies in African populations; these population are generally under-represented in existing genomics databases. They found that, depending on cost considerations and study goals, that low-pass sequencing in the range of 0.5x to 4x coverage outperformed a wide range of genotyping arrays.

    The $100 Genome: Using Low-Pass Whole Genome Sequencing as an Alternative to Genotyping Arrays

    In this webinar originally presented at the ASHG 2020 Virtual Meeting, learn how low-pass WGS overcomes the inherent limitations and biases of traditional arrays, offering an inexpensive, high-throughput alternative for detecting genome-wide genetic variation and novel variants.

    Workshop & Roundtable Discussion | Exploring Bioinformatics for Whole Genome Sequencing (WGS) Data

    In this recording of our WGS bioinformatics workshop & roundtable discussion led by bioinformatics scientist Zain Alvi, Ph.D., we'll guide you through the WGS bioinformatics process to help you learn to interpret WGS bioinformatics results, as well as address common challenges and answer frequently asked questions (FAQs).


Azenta is a certified service provider for Illumina and other cutting-edge NGS platforms. For information on our NGS platforms as well as recommended configurations of your projects, please visit the NGS Platforms page. Azenta does not guarantee data output or quality for sequencing only projects.

How To Order

Email | Phone 1-877-436-3949, Ext. 1