Explore a new paradigm in sequencing with HiFi reads
Advanced scientific discoveries require sequencing data that is both accurate and complete. PacBio sequencing technology has evolved to a different type of long read, known as highly accurate long reads, or HiFi reads.
PacBio is the only sequencing technology to offer HiFi reads that provide accuracy of 99.9%, on par with short reads and Sanger sequencing. With HiFi reads you no longer compromise long read lengths for high accuracy sequencing to address your toughest biological questions.
How it works Watch HiFi explained
Benefits of HiFi sequencing
Long reads
Up to 25 kb in length
High accuracy
Sequencing free of systematic errors
Uniform coverage
No bias even for high GC regions
Epigenetics
Direct methylation without special library prep
Video
Hear what our customers are saying about HiFi
Discover how HiFi sequencing is transforming research directly from the scientists who use the technology. It’s more than just about long read lengths and high accuracy—it’s about making a real impact in the field.
Breakthroughs in HiFi discovery
Blog
Sequencing 101: long-read sequencing
Long-read sequencing technologies such as PacBio HiFi sequencing are quickly becoming the new gold standard in genomics research. This article provides an introductory look at what long-read sequencing is, and explores topics including advantages, applications, and more.
This is your moment for a more complete view of biology
Comprehensive variant calling with phasing + 5mC
Access high accuracy for all variant types — SNVs, indels, structural variants, tandem repeat expansions, and methylation — including in challenging regions.
Truly complete assembly of complex genomes
Accurately construct the full sequence of chromosomes, including telomeres and centromeres.
Targeted sequencing to study genes at scale
Focus the power of HiFi variant calling by enriching for regions of interest using hybrid capture or PCR amplification.
Single-cell transcriptome sequencing
Catalog RNA isoforms at single-cell resolution, moving beyond gene counting to catalog full length transcripts.
How HiFi sequencing compares
HiFi Difference blog series
From eye-opening tech comparisons to inspiring examples of PacBio HiFi technology in action, this blog series explores what sets HiFi sequencing apart.
Frequently asked questions about HiFi
HiFi sequencing combines long reads (500–20,000 bases) with 99.9% read accuracy, delivering comprehensive, high-confidence genomic and epigenomic insight in a single run.
Unlike short reads (typically 150–200 bp), HiFi reads can span:
- Structural variants
- Repetitive and GC-rich regions
- Segmental duplications
- Medically relevant “dark” genes
Because HiFi sequences native DNA without PCR, it detects:
- All major variant types
- Haplotype phasing
- DNA methylation (5mC, 5hmC, 6mA)
- Genetic and epigenetic information simultaneously
For RNA applications, HiFi long reads capture full-length isoforms, enabling accurate transcript and splice variant characterization, without assembly guesswork.
HiFi is the only known sequencing technology delivering the gold standard in native long reads accurate enough to trust, and long lengths that truly span SVs and complex regions.
Interested in getting a deeper understanding of what the advantages and applications of native long read sequencing? Start reading here.
While multiple platforms offer long reads, HiFi stands out for:
High per-read accuracy
Each read is highly accurate on its own—reducing false positives and simplifying downstream analysis.
Lower coverage requirements
~20× coverage is typically sufficient for confident variant and methylation calls, compared to ~40× for other long-read methods.
Smaller data files
A typical HiFi human genome BAM file is ~30–60 GB, versus >1,300 GB for other nanopore datasets, reducing storage and compute burden.
Lower DNA input
With SPRQ chemistry, native whole genome sequencing requires just 500 ng of DNA. The Ampli-Fi protocol supports inputs as low as 1 ng.
Interested in learning more about the differences between long-read sequencing technologies? Read more.
HiFi sequencing detects methylation directly from native DNA, automatically, in every run—no extra assays required.
It works by measuring subtle changes in polymerase kinetics as modified bases (such as 5mC) are incorporated during sequencing.
This enables:
- Direct, nucleotide-level methylation detection
- Simultaneous variant + methylation analysis
- 5-base multiomic sequencing in a single assay
In contrast, short-read platforms typically require separate methods such as bisulfite sequencing (which can damage DNA) or arrays (which sample only a fraction of CpG sites).
With HiFi—and advanced assays like Fiber-seq—researchers can link genetic variation, methylation, and chromatin accessibility at single-molecule resolution.
The cost gap between long-read and short-read sequencing has narrowed significantly.
Human whole genome sequencing (20× coverage)
~$345 per human genome on the Revio system with SPRQ-Nx chemistry, using as little as 500 ng input.
Transcriptomics (isoform-level analysis)
Typically a few hundred dollars per sample, delivering full-length isoform resolution—not just gene-level counts.
Microbial genomes
Often tens of dollars per sample, yielding reference-grade closed genomes plus methylation data.
Full-length 16S and amplicons
Per-sample costs can drop to just a few dollars while achieving species- and strain-level resolution.
With the Vega benchtop system, HiFi long reads are also accessible in-house for individual labs.
Would you like to speak to someone about your project and pricing needs? Fill out the form and we will be in touch soon.
HiFi sequencing now supports flexible, accessible input requirements:
- Whole genome sequencing: 500 ng DNA (SPRQ chemistry)
- Low-input workflows (Ampli-Fi): 1 ng DNA
- Isoform sequencing: 300 ng total RNA
- Single-cell cDNA: as little as 15 ng
PacBio Nanobind extraction kits streamline high molecular weight DNA isolation across sample types, and workflows are automation-ready for scale.
Compared to other long-read platforms that may require 1–2 µg of high molecular weight DNA, HiFi operates in a more accessible input range.
HiFi sequencing is the only known long-read technology to provide 99.9% or better accuracy in every run. With over 1,000 peer-reviewed publications in 2023 alone and over 1,200 HiFi sequencers globally, the PacBio portfolio of reliable and established sequencing systems includes both the production-scale Revio and the Vega benchtop system. Our Powered by PacBio blog series discusses the latest notable research and publications.
