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).
Human whole genome sequencing
Completely characterize human genomes to better understand the complexity of health and disease.
Plant + animal whole genome sequencing
Quickly and affordably produce contiguous, complete, and correct de novo assemblies of even the most complex genomes.
Microbial whole genome sequencing
Achieve closed chromosomes and plasmids from even the most repeat-dense and GC-rich genomes.
Whole genome sequencing — how PacBio compares
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.
SHAPING THE FUTURE
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.
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.
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.
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 |
HiFi reads directly identify base modifications
HiFi sequencing provides epigenetic information during a normal sequencing run, without any special library preparation required.
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.
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.
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.
Epigenetics
HiFi sequencing equips you to capture epigenetic modifications during a normal sequencing run — no special chemistry or preparation required.
Whole genome sequencing in action
Case Study
Pioneering a pangenome reference collection
Learn about DuPont Pioneer’s ambitious plant pan-genome reference project.
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.
Bacterial genomes from the lakes of Minnesota to NYC hospitals
See how scientists are studying the ecophysiology of Minnesota microbes using long-read…
Uncovering structural variants associated with rare disease
Discover how Alexander Hoischen’s research group is using long-read sequencing to find…
EXPLORE
Did you know we have a comprehensive library of articles, reports, papers, and videos related to whole genome sequencing?
Whole genome sequencing workflow at a glance
Easy-to-use, high throughput sequencing for the accuracy you need at an affordable cost
Straightforward library prep
Go from sample to sequencer in a single afternoon
Complete + accurate sequencing
Obtain accurate, unbiased, and long reads
Directly detect epigenetic modifications
Universal file types
Analyze data using any of the common genome assembly and analysis tools
Common questions about PacBio whole genome sequencing
SUGGESTED WHOLE GENOME SEQUENCING PRODUCTS
Nanobind kits for DNA extraction
SMRTbell prep kit 3.0 for library prep