Plant and Animal Low-Pass Whole Genome Sequencing

Plant and Animal Low-Pass Whole Genome Sequencing

Service Description

Plant and animal low pass whole genome sequencing (lpWGS) involves sequencing the entire genome of a plant/animal species at low sequencing depth. LpWGS provides a more comprehensive, accurate and efficient tool for large-scale genomics projects that traditionally have used legacy technology such as genotyping arrays. The lpWGS approach outperforms the arrays by providing an order of magnitude more data, greater statistical power, and enhanced variant discovery capabilities.

Genotyping-by-sequencing (GBS) is another common technique used in plant or animal genomic studies. While cost effective, GBS produces extensive missing data and requires complex bioinformatics analysis.

Our end-to-end workflow can support you with a broad range of species: cattle, pig, chicken, dog, cat, rat, mice, corn, rice, soybean and pea. We also evaluate and accept custom projects on a case-by-case basis. We can perform deep sequencing for a select number of individuals and build a well assembled reference genome for imputations.

DNBSEQ™ Sequencing and Gencove Imputation 

The unique combination of DNBSEQ™ sequencing and Gencove ImputeSeqTM low-pass imputation pipeline enables researchers to efficiently obtain fully-imputed, analysis-ready VCF files from DNA in a single service.


Essentially, the genome is shotgun sequenced at a very low depth (between 0.4x and 1x) by the DNBSEQ™ platform in lpWGS and the raw sequence data is then uploaded to a proven imputation pipeline. This results in over 99% accurate variant calls across the whole genome while ancestry and microbiome profiles are also provided, all at the cost of a common genotyping array or less.

Benefits of Low-Pass Sequencing

  • A single assay replacing all common arrays
  • More than 99% accurate whole genome variant calls
  • High-throughput and cost-effective
  • Flexible set-up of new species or custom populations
  • Rare variant discovery
  • Low DNA inputs required


Sequencing Platform

BGI Low-Pass Whole Genome Sequencing services are executed with the DNBSEQ™ sequencing technology, for great sequencing data at the lowest cost in the industry.

DNBSEQ™ is BGI’s proprietary sequencing technology, developed by our Complete Genomics subsidiary in Silicon Valley.


Project Workflow

We care for your samples from the start through to the result reporting. Highly experienced laboratory professionals follow strict quality procedures to ensure the integrity of your results.

  • Sample QC
  • Library QC
  • Sequencing QC
  • Data QC
  • Sample Preparation
  • WGS Library Preparation
  • Sequencing
  • Raw Data Output
  • Bioinformatics Analysis

How to order

We care for your samples from the start through to the result reporting. Highly experienced laboratory professionals follow strict quality procedures to ensure the integrity of your results.

Request a Quote

Send us a no obligation request for quote and our dedicated sales team will reply to you within 24 hours.

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Sequencing Service Specification

BGI Plant & Animal Genome Sequencing Services are performed with BGI’s DNBseq sequencing technology, featuring DNA Nanoballs, linear Rolling Circle Replication and cPAS technology for superior data quality.

    • PCR and PCR-free library methods are available
    • 100bp and 150bp paired-end sequencing available
    • Raw data, standard and customized data analysis
    • Available data storage and bioinformatics applications
  • Sequencing Quality Standard

    Sequencing Quality Standard

    • Guaranteed ≥80% of clean bases with quality score of ≥Q30
  • Turn Around Time

    Turn Around Time

    • Typically, 45 working days from sample QC acceptance to data analysis report availability
    • Expedited services are available; contact your local BGI specialist for details

Sample Requirements

We can process your gDNA, whole blood, cell line, fresh frozen tissue, and FFPE samples from a variety of species, with the following general requirements:

DNA Amount and Concentration

Minimum Sample Volume

Regular Samples

Intact genomic DNA ≥ 1μg, Concentration ≥ 12.5ng/μl

15 μl

Low Input Samples

Intact genomic DNA ≥ 200ng, Concentration ≥ 2.5ng/μl

15 μl

True PCR-Free

Intact genomic DNA ≥ 1.5μg, Concentration ≥ 12.5ng/μl

15 μl

Data Analysis

Besides clean data output, BGI offers a range of standard and customized bioinformatics pipelines for your low pass whole genome sequencing project. Reports and output data files are delivered in these file formats: FASTQ, BAM, VCF, JSON, and TXT.


  • Data filtering

  • Read alignment

  • SNP calling

  • Imputation

  • CNV analysis

  • Lineage

  • Microbiome


Further customization of bioinformatics to suit your unique project, including GWAS analysis and SNP annotation, is available.
Please contact your BGI technical representative for details.

Low-Pass WGS Resources

Read or download Low-Pass Whole Genome Sequencing documentation and data. Don't find what you need right away? Please contact your local BGI representative.

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