Whole genome sequencing

A complete view of the genome to fuel research and discovery

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Whole genome sequencing

Whole genome sequencing (WGS) evaluates the full DNA content of an organism — be it human, plant, animal, or microbe. PacBio HiFi sequencing has exceptionally accurate long reads and unbiased coverage required to provide a truly comprehensive view.

HiFi sequencing delivers whole genome sequence information with complete and accurate resolution through unbiased, single-molecule reads of up to 25 kb, a median read accuracy of >99.9% (Q30), and the ability to sequence through repeats and GC-rich regions:

Complete, contiguous, correct, and phased genome assemblies

HiFi read length and accuracy resolve even the most difficult repeats — segmental duplications and centromeres — to produce genomes with longer contigs, fewer fragmented genes, and the correct sequence of all regions.

Highest precision and recall for variant calling

Only HiFi sequencing enables the highest precision and recall for calling variants of all types: single-nucleotide variants (SNVs), small insertions and deletions (indels), and structural variants (SVs).

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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

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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Whole genome sequencing — how PacBio compares

PacBio HiFi Illumina Oxford Nanopore
Average read length1
15–20 kb
2 x 150 bp 10–100 kb
Average read accuracy1
99.95% (Q33) 99.92% (Q31) 99.26% (Q21)
Unbiased Reduced at low and high [GC] Reduced in low-complexity runs
Variant calling: SNVs
Variant calling: indels
Variant calling: SVs
Genome assembly: contiguity
Genome assembly: accuracy
Epigenetics: 5mC

1. PacBio HiFi: HG003 18 kb library, Sequel II system chemistry 2.0, precisionFDA Truth Challenge V2 (, Illumina: HG002 2×150 bp NovaSeq library, precisionFDA Truth Challenge V2 (, ONT: Q20+ chemistry (R10.4, Kit 12), Oct 2021 GM24385 Q20+ Simplex Dataset Release (
2. HiFi+ONT: Nurk 2021, HiFi+Illumina: Logsdon 2020, ONT: Tan 2022

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Whole genome sequencing best practices

Access this guide to learn how to achieve successful de novo whole genome sequencing and assembly for complex plant and animal genomes.

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In PrecisionFDA Challenge, PacBio Hifi reads outperform both short reads and noisy long reads

PacBio HiFi reads delivered the highest precision and recall in all categories: genome-wide, specifically in difficult-to-map regions, and in the major histocompatibility complex.

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HiFi reads reveal unique insights at the whole genome level

  • Genome coverage is more uniform. HiFi reads are generated without amplification, ensuring uniform coverage regardless of GC content.
  • Long-range phasing is accurate. Long, accurate reads ensure you have the highest confidence in phasing haplotypes and identifying compound heterozygous variants, even when variants are separated by tens of kilobases.
  • “Difficult” regions can be sequenced. HiFi reads accurately resolve long repeats, homopolymer stretches, and segmental duplications.

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HiFi Reads simplify analysis of whole genome sequencing data

  • Complete genome assembly is quicker and easier. Assemble a microbial genome in minutes and a human genome in a single day on a single computer.
  • Assembled genomes are more complete. Unlock 15% of the genome that is otherwise inaccessible with short reads.
  • Phasing haplotypes is straightforward. Long, accurate reads simplify haplotype phasing without having to rely on inference or sequence data from additional individuals.

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Whole genome sequencing datasets

Application Dataset Data type PacBio system
Variant detection, assembly, epigenetics Homo sapiens – GIAB trio HG002-4 HiFi reads Revio system
Tumor/normal COLO829 melanoma HiFi reads Revio system
Whole genome sequencing Various plant & animals – maize, mouse, and others HiFi reads Revio system
Assembly (ultra-low DNA input) Phlebotomus papatasi, Homo sapiens, Drosophila melanogaster HiFi reads Sequel II system
Assembly Food safety and infectious microbes – 96 plex HiFi reads Sequel II system

More datasets

HiFi reads directly identify base modifications

HiFi sequencing provides epigenetic information during a normal sequencing run, without any special library preparation required.

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Whole genome sequencing applications

Variant detection

From SNVs to structural rearrangements, highly accurate single-molecule long reads allow you to confidently catalog variants of all kinds.

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De novo sequencing

With HiFi reads up to 25 kb, you can efficiently and affordably generate de novo assemblies of even the most complex genomes.

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Genome structure

HiFi data delivers insights into genome structure that short-read technologies often miss. Generate long reads, even through highly repetitive regions of the genome.

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HiFi sequencing equips you to capture epigenetic modifications during a normal sequencing run — no special chemistry or preparation required.

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Whole genome sequencing in action

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Scaling human whole genome sequencing for rare and inherited disease research

Find out how PacBio HiFi whole genome sequencing is being used in rare disease research.

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Bacterial genomes from the lakes of Minnesota to NYC hospitals

See how scientists are studying the ecophysiology of Minnesota microbes using long-read…


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Uncovering structural variants associated with rare disease

Discover how Alexander Hoischen’s research group is using long-read sequencing to find…


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Did you know we have a comprehensive library of articles, reports, papers, and videos related to whole genome sequencing?

Explore resources

Whole genome sequencing workflow at a glance

Easy-to-use, high throughput sequencing for the accuracy you need at an affordable cost

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Straightforward library prep

Go from sample to sequencer in a single afternoon

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Complete + accurate sequencing

Obtain accurate, unbiased, and long reads

Directly detect epigenetic modifications

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Universal file types

Analyze data using any of the common genome assembly and analysis tools

Common questions about PacBio whole genome sequencing

HiFi reads provide the most comprehensive view of human genomes with the highest precision and recall for all variant types including variants missed by short-read sequencing: small variants in difficult-to-map regions of the genome and structural variants genome-wide. HiFi reads also phase variants into maternal and paternal haplotypes.

Yes, HiFi sequencing is able to 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.

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