Whole genome sequencing

Whole genome sequencing (WGS) with PacBio HiFi sequencing delivers a more complete and accurate genome with long, single-molecule reads and 90% of bases at ≥Q30.

Contiguous and phased genome assemblies

The unique combination of length and accuracy enables HiFi reads to resolve difficult repeats, segmental duplications, and centromeres to produce more contiguous and phased assemblies.

Precision and recall for variant calling

HiFi reads also provide precisionFDA-winning accuracy for all variant types, especially in the most challenging parts of the human genome.

Methylation calling

HiFi sequencing also provides simultaneous 5mC and 6mA detection without any additional library preparation. This feature enables the resolution of methylation profiles with phased haplotyping and the ability to interrogate methylation abnormalities from a single sequencing experiment.

Human whole genome sequencing

Completely characterize human genomes to better understand the complexity of health and disease.

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Plant + animal whole genome sequencing

Quickly and affordably produce contiguous, complete, and correct de novo assemblies of even the most complex genomes.

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Microbial whole genome sequencing

Achieve closed chromosomes and plasmids from even the most repeat-dense and GC-rich genomes.

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Common questions about PacBio whole genome sequencing

Whole genome sequencing (WGS) is a powerful DNA sequencing technology that determines the complete genetic sequence of an organism’s genome. Every living organism has a unique genetic code made up of four nucleotide bases—adenine (A), thymine (T), cytosine (C), and guanine (G). WGS analyzes all of this DNA, including both coding genes and non-coding regions, to provide a comprehensive view of genetic variation, mutations, and biological function.

WGS plays a critical role in genomics, genetic research, and precision medicine. In human health, whole genome sequencing helps identify inherited diseases, uncover disease mechanisms, track infectious pathogens, and enable personalized treatments.

In plant and animal research, WGS supports the discovery of climate-resilient traits, improves breeding programs, enhances disease resistance, and helps preserve genetic diversity.

In microbial genomics and public health, WGS is used to track outbreaks of infectious diseases, analyze microbiomes in humans and the environment, and identify new biochemical pathways that can advance biotechnology and improve human health.

By delivering a complete picture of an organism’s DNA, whole genome sequencing is one of the most important tools for genome analysis, biotechnology innovation, and advanced genetic testing.

HiFi sequencing delivers high-accuracy long reads that transform whole genome sequencing (WGS). By combining >99.9% accuracy (Q30–Q40) with long read lengths (10–25+ kb), HiFi technology enables researchers to generate complete, phased, and highly reliable genomes in a single workflow.

Compared to short-read sequencing technologies, the long read length of HiFi sequencing can bridge through repetitive and low complexity regions in the genome. Many of these challenging regions of the human genome contain medically relevant genes, and HiFi can provide the most comprehensive sequencing results compared to short reads. Further, short reads cannot phase through distant regions on the genome or provide methylation information without additional library preparation.

Compared to other long-read sequencing technologies, the higher accuracy of HiFi reads means less sequencing depth is required for accurate variant detection in whole gnome sequencing in a cost-effective manner.

To learn more, read the Sequencing 101 blog.

Yes, HiFi sequencing can simultaneously determine the identity and methylation status of individual bases in a DNA molecule. The methylation calling relies on kinetic properties (pulse width and interpulse duration) of the sequencing polymerase. A statistical model processes the kinetic information to infer methylation status.

Unlike most sequencing technologies, HiFI WGS provides methylation information without the need for additional library preparation (e.g. bisulfite sequencing), and is therefore more cost-effective.

HiFi currently offers 5-methylcytosine (5mC) and N6-methyladenine (6mA) methylation calling, however, 5-hydromethylcytosine (5hmC) will also be enabled soon.

To learn more, visit https://pacb.com/epigenetics

Whole genome sequencing datasets

Application	Dataset	Download literature	Technology	Sequencing system
Variant detection, assembly, epigenetics	Homo sapiens — GIAB trio HG002-4	Application note	HiFi long read	Revio system
Tumor/normal	COLO829 melanoma	Application note	HiFi long read	Revio system
Tumor/normal	HCC1395	Application note	HiFi long read	Revio system
Whole genome sequencing	Various plant & animals – mouse, ladybug, oak, mistletoe, and maize	Plant + animal biology	HiFi long read	Revio system
Assembly	Food safety & infectious microbes – 96 plex	Microbial WGS	HiFi long read	Sequel IIe system

More datasets

Whole genome sequencing in action

Publication

HiFi powers the 1000 Chinese Pangenome study

The 1000 Chinese Pangenome (1KCP) project utilized HiFi to sequence 1,116 Chinese whole genomes to construct a pangenome that included novel sequences not present in existing references and an expanded catalog of variants in medically relevant regions.

Read the paper

SPRQ Your Research: Expert insights & workflows

The Revio SPRQ chemistry is advancing all aspects of long-read sequencing. Listen to expert users like Lutz Froenicke from UC Davis and Shawna McDevitt from UC Berkeley on how they’re using HiFi sequencing to deliver the best genomes to their customer.

Watch video

SPRQ-Nx chemistry and multiomics applications for plant & animal research

Hear how the upcoming SPRQ-Nx chemistry will allow SMRT Cell re-use, further reducing the cost of whole genome sequencing. Plus, hear how Fiber-seq is used to study chromatin accessibility, while Ci-Fi is the HiFi version of 3C (chromatic conformation capture) – all to create the highest quality of genome assemblies for plant & animal research.

Watch video

WGS helps uncover hidden drivers of Alzheimer’s risk

Comparing the HiFi genomes of 245 Alzheimer’s disease (AD) samples and 248 centenarians without AD identified structural variations and methylation patterns potentially associated with the disease.

Read the paper