Support FAQs

Our Certified Service Providers (CSPs) deliver high-quality sequencing services using PacBio technology around the world. While PacBio doesn’t perform sequencing directly, you can easily find a CSP near you to get your samples processed.

Email support@pacb.com with your employer or institution name and address and we will connect you with the appropriate PacBio sales or support team for your region.

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 offers a streamlined, end-to-end workflow—from sample to analysis.

Start with high-molecular-weight DNA extraction using Nanobind DNA kits, delivering quality DNA from a wide range of sample types in about two hours. DNA is then converted into SMRTbell libraries using manual or automation-friendly prep kits.

Libraries are loaded onto Vega or Revio systems, with simple run setup in SMRT Link software.

After sequencing, advanced algorithms—including Google Health DeepConsensus accelerated by NVIDIA GPUs—process data onboard to generate highly accurate HiFi reads. Outputs are delivered in standardized BAM format, ready for genome assembly, variant detection, phasing, and other downstream analyses.

This unified workflow reduces complexity and accelerates time to insight.

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.

Explore PacBio Epigenetic solutions

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.

HiFi data combine long read lengths (typically 15–25 kb) with Q30+ accuracy, they can be used directly in many standard bioinformatics workflows:

• De novo genome assembly – Produces highly contiguous assemblies with fewer gaps and more complete resolution of repetitive regions.

• Structural variant (SV) detection – Accurately identifies large insertions, deletions, inversions, and complex rearrangements.

• Small variant calling (SNVs and indels) – High accuracy supports confident detection of single-nucleotide and small insertion/deletion variants.

• Haplotype phasing – Long reads span multiple variants, enabling accurate phasing across extended genomic regions.

• Full-length transcript sequencing (Iso-Seq analysis) – Captures complete transcript isoforms without assembly.

• Epigenetic modification detection – Native DNA sequencing enables direct detection of base modifications.

Because HiFi reads reduce ambiguity in complex genomic regions, they simplify pipelines that traditionally required hybrid sequencing approaches or extensive validation—accelerating time from data generation to biological insight.

Explore popular tools and workflows for HiFi applications

Explore example datasets with the applications and tools

HiFi sequencing does not require PCR amplification because it is a single-molecule, real-time (SMRT) sequencing technology. Instead of copying DNA millions of times before sequencing, HiFi reads are generated by observing a single native DNA molecule as a DNA polymerase synthesizes it in real time.

Each DNA fragment is converted into a circular SMRTbell template. During sequencing, the polymerase makes multiple passes around the same molecule. These repeated observations are combined through Circular Consensus Sequencing (CCS) to produce a highly accurate HiFi read (Q30+), without the need for amplification.

Avoiding PCR provides several advantages:

• Reduced amplification bias, including improved representation of GC-rich or complex regions

• More uniform genome coverage

• Preservation of native DNA characteristics

• Direct detection of base modifications

By achieving accuracy through consensus of multiple passes—rather than amplification—HiFi sequencing delivers long, highly accurate reads while maintaining the integrity of the original DNA molecule.

The total time from DNA sample to HiFi reads typically ranges from a few days, depending on the application and system used.

• DNA extraction: ~2 hours using Nanobind kits

• Library preparation: ~1 day

• Sequencing run: Hours to ~1 day, depending on insert size and system (Vega or Revio)

• Data processing: onboard processing is performed automatically, generating highly accurate HiFi reads shortly after the run completes

Because HiFi reads are produced with Q30+ accuracy, downstream analysis often requires fewer correction steps compared to other long-read methods—helping researchers move quickly from raw DNA to actionable biological insight.

Outputs are delivered in standardized BAM format, ready for genome assembly, variant detection, phasing, and other downstream analyses.

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.

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.

No. PacBio does not charge for using SMRT Link Cloud. All core features, including run design, instrument monitoring, and run setup, are completely free with no usage limits. You are only responsible for any storage or analysis costs from your chosen third-party providers.

SMRT Link Cloud includes the same core features for instrument management, run setup, and monitoring as the local version of SMRT Link. However, SMRT Link Cloud does not include SMRT Analysis. Instead, it connects directly to your chosen storage so you can use external or third-party analysis tools.