HiFi Sequencing – Unlock Your Next Great Discovery
With HiFi Sequencing you get the benefits of short reads and traditional long reads in one easy-to-use technology. Watch this short video to learn how HiFi Sequencing is empowering scientists to strive for new breakthroughs.
Explore A New Paradigm in Sequencing with HiFi Reads
Advanced scientific discoveries require sequencing data that is both accurate and complete. Single Molecule, Real-Time (SMRT) 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 have to compromise long read lengths for high accuracy sequencing to address your toughest biological questions.
What are HiFi Reads?
HiFi reads are a type of data produced using the circular consensus sequencing (CCS) mode on one of the PacBio Sequel Systems. HiFi reads provide base-level resolution with >99.9% single-molecule read accuracy.
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HiFi reads can be used across a wide range of SMRT Sequencing applications, from whole genome sequencing for de novo assembly, comprehensive variant detection, RNA sequencing and more. |
How are HiFi Reads Generated?
How are HiFi Reads Different from Traditional PacBio Long Reads?
HiFi reads are produced by calling consensus from subreads generated by multiple passes of the enzyme around a circularized template. This results in a HiFi read that is both long and accurate. In contrast, traditional PacBio long reads are generated by a single pass of the enzyme around a circularized template, which although allows for overall longer read lengths, does not provide the high accuracy characteristic of HiFi reads. Learn more about how SMRT Sequencing works.
How Does HiFi Sequencing Compare with Other Technologies?
HiFi reads let you accurately detect all types of variants, from single nucleotide to structural variants, with high precision and recall and phase haplotypes, even in hard-to-sequence regions of the genome. Explore the resources below for more information on how HiFi reads perform relative to other technologies.
Original Publication: Wenger, A. M., et al. (2019) Accurate Circular Consensus Long-read Sequencing Improves Variant Detection and Assembly of a Human Genome. Nature Biotechnology, 37, 1155–1162.
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The Telomere-to-Telomere (T2T) Consortium selected HiFi sequencing to generate the first fully complete human genome assembly, 20 years after the original human genome project. |
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HiFi reads make understanding the accuracy of your sequencing data easy and straight forward, but there is a lot to know about accuracy when considering a sequencing technology. |
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In the precisionFDA Truth Challenge V2, which evaluated methods for variant calling in human genomes, approaches that use HiFi reads delivered the highest precision and recall in all categories.
Read the Blog Post to Learn More or Watch a Short Video to Understand Results from the precisionFDA Truth Challenge |
What are the Benefits of HiFi Sequencing?
There are many advantage to using HiFi sequencing beyond the long read lengths and high accuracy. These include easy library preparation, low coverage requirements, small file sizes, and the fastest time to assembly. Explore the resources below better understand these advantages.
Learn more about the benefits of HiFi reads and see how they provide a single technology solution across a range of applications
Hear from PacBio users on how they are employing HiFi reads to explore genomes, transcriptomes, and metagenomes and the benefits HiFi reads provide for addressing their critical life science questions.
Discover the Many Ways Scientists are Using HiFi Reads in Their Research:
- A Genome Fit for a Giant — Sequencing the California Redwood
- PacBio HiFi Reads: ‘Most Effective Stand-Alone Technology for De Novo Assembly’
- A HiFi view – Sequencing the Gut Microbiome with Highly Accurate Long Reads
- Variant Calling and De Novo Genome Assembly with PacBio HiFi Reads
- New Sequel II System Enables Rapid Characterization of Invasive Pests
Find many more examples or try working with HiFi read data yourself in the SMRT Resources library.
How to Get Started with HiFi Sequencing?
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Learn more about HiFi sequencing using the award-winning Sequel Systems |
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Connect with a PacBio scientist to have your questions answered or for a free project consultation
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Contact a PacBio Certified Service Provider to run a sequencing project from start to finish |
Selected Resources
- Wenger, Aaron M et al. (2019) Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nature biotechnology
- Zhang, Xiujuan et al. (2019) Full-length transcriptome analysis of Litopenaeus vannamei reveals transcript variants involved in the innate immune system. Fish & shellfish immunology
- Mizuguchi, Takeshi et al. (2019) Detecting a long insertion variant in SAMD12 by SMRT sequencing: implications of long-read whole-genome sequencing for repeat expansion diseases. Journal of human genetics
- Mayor, Neema P et al. (2019) Recipients receiving better HLA-matched hematopoietic cell transplantation grafts, uncovered by a novel HLA typing method, have superior survival: A retrospective study Biology of Blood and Marrow Transplantation
- Kosicki, Michael et al. (2018) Repair of double-strand breaks induced by CRISPR-Cas9 leads to large deletions and complex rearrangements. Nature biotechnology
- Nattestad, Maria et al. (2018) Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line. Genome research
- Kronenberg, Zev N et al. (2018) High-resolution comparative analysis of great ape genomes. Science
- Ardui, Simon et al. (2018) Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics. Nucleic acids research
- Poster: Kingan, Sarah et al. (2021) HiFiViral SARS-CoV-2: A Kitted Solution for Genome Surveillance that is Robust Across Sample Input Quantities and New Variants
- Poster: Zhu, Lei et al. (2021) Full-Length Sequencing of CYP2D6Variants with PacBio HiFi Reads
- Poster: Rowell, William J. et al. (2020) Comprehensive variant detection in a human genome with highly accurate long reads
- Poster: Rowell, William J. et al. (2020) A workflow for the comprehensive detection and prioritization of variants in human genomes with PacBio HiFi reads
- Poster: Portik, Daniel et al. (2020) Metagenomic analysis of type II diabetes gut microbiota using PacBio HiFi reads reveals taxonomic and functional differences
- Poster: Wenger, Aaron M. et al. (2020) Copy-number variant detection with PacBio long reads
- Poster: Ashby, Meredith et al. (2020) Unbiased characterization of metagenome composition and function using HiFi sequencing on the PacBio Sequel II System
- Poster: Tseng, Elizabeth et al. (2020) A complete solution for high-quality genome annotation using the PacBio Iso-Seq method
- Poster: Galvin, Brendan et al. (2020) A high-quality PacBio insect genome from 5 ng of input DNA
- Poster: Kingan, Sarah B. et al. (2020) Beyond Contiguity: Evaluating the accuracy of de novo genome assemblies
- Poster: Kingan, Sarah B. et al. (2020) Every species can be a model: Reference-quality PacBio genomes from single insects
- Poster: Wenger, A.M. et al. (2019) Comprehensive structural and copy-number variant detection with long reads
- Poster: Rowell, W. J. et al. (2019) Detection and phasing of small variants in Genome in a Bottle samples with highly accurate long reads
- Poster: Tseng, E. et al. (2019) Full-Length RNA-seq of Alzheimer brain on the PacBio Sequel II System
- Poster: Kronenberg, Z. N. et al. (2019) High-quality human genomes achieved through HiFi sequence data and FALCON-Unzip assembly
- Poster: Neveling, K. et al. (2019) The value of long read amplicon sequencing for clinical applications
- Poster: van Min, M. et al. (2019) TLA & long-read sequencing: Efficient targeted sequencing and phasing of the CFTR gene
- Poster: Ekholm, J. et al. (2019) Sequencing the previously unsequenceable using amplification-free targeted enrichment powered by CRISPR/Cas9
- Poster: Ashby, Meredith et al. (2019) Unbiased characterization of metagenome composition and function using HiFi sequencing on the PacBio Sequel II System
- Poster: Jain, S. et al. (2019) Comparison of sequencing approaches applied to complex soil metagenomes to resolve proteins of interest
- Poster: Rowell, W. J. et al. (2019) Comprehensive variant detection in a human genome with highly accurate long reads
- Poster: Peluso, Paul et al. (2019) Single molecule high-fidelity (HiFi) Sequencing with >10 kb libraries
- (2021) PacBio HiFiViral SARS-CoV-2 Kit
- Tsai, Yu-Chih (2021) A High-Resolution Panel for Uncovering Repeat Expansions that Cause Ataxias
- Kingan, Sarah (2021) HiFiViral: A Novel Method for Surveillance of SARS-CoV-2 that is Robust Across Sample Input Quantities and the Evolution of New Variants
- Wenger, Aaron (2021) Methylation Detection with PacBio HiFi Sequencing
- Gonzaludo, Nina (2021) Using HiFi Reads for Improved and Accurate Haplotyping and Phasing of Pharmacogenomic Alleles
- Henry, Christian and Shen, Richard and Stone, Jennifer (2021) With Long Reads and Short Reads, the Possibilities are Endless – PacBio ASHG 2021 Fireside Chat
- Stone, Jennifer (2021) HiFi Sequencing: See What You’ve Been Missing
- Farrow, Emily (2021) Integrated Rare Disease using Long-Read Genome Sequencing
- Al’Khafaji, Aziz (2021) Scalable RNA Isoform Sequencing using Intramolecular Multiplexed cDNAs
- Holstege, Henne (2021) Uncovering Neurological Disorders Through an Examination of VNTRs
- Ashby, Meredith and Fiske, Haley (2021) SFAF NGS Tech Panel
- Crawford, Seth and Feldmann, Mitchell and Vierra, Michelle and Ware, Doreen (2021) Getting the Most Out of Your Breeding Program with DNA and RNA Sequencing
- Lovell, John (2021) Four Chromosome Scale Genomes and a Pan-Genome Annotation to Accelerate Pecan Tree Breeding
- Kolmogorov, Mikhail (2021) Generation of Lineage-Resolved Complete Metagenome-Assembled Genomes in Complex Microbial Communities
- Ashby, Meredith; Bickhart, Derek, and Portik, Dan (2021) Revealing Mechanisms of Bacterial Virulence and Adaptation with PacBio SMRT Sequencing
- Hiatt, Susan and Korlach, Jonas (2021) Long-Read Genome Sequencing for the Molecular Understanding of Neurodevelopmental Disorders
- Ashby, Meredith and Brown, Candice and Driscoll, Mark and Leung, Elaine (2021) Identifying Key Players in Host-Microbiome Interactions with High Resolution 16S Sequencing
- Ashby, Meredith; and Boritz, Eli (2021) Resolving Viral Evolution and Quasispecies Diversity with HiFi Sequencing
- Ashby, Meredith; Bickhart, Derek, and Portik, Dan (2021) Optimizing for Information: What Richer Data and Better Assemblies Reveal About Metagenome Structure and Function
- Tai, Phillip (2021) AAV-Genome Population Sequencing of Vectors Packaging CRISPR Components Reveals Design-Influenced Heterogeneity
- Joglekar, Anoushka (2021) A Spatially Resolved Brain Region and Cell Type-Specific Isoform Atlas of the Postnatal Mouse Brain
- Levy, Shawn and Heiner, Cheryl and Aro, Lori (2021) Transformative Drug Research and Development via Accurate and Scalable Long-Read Sequencing Services
- Aro, Lori and Scott, Stuart A and Yang, Yao (2021) Advancing Pharmacogenomics Research and the Need for Highly Accurate Long-Read Sequencing
- Blethrow, Justin and Smith, Melissa L. and Vinnere Pettersson, Olga (2021) Webinar: Unleashing the Power of HiFi Sequencing – How the Sequel IIe System Removes Barriers and Empowers Life Scientists
- Miller, Dave and Hernandez, Alvaro (2021) Creating Core Demand with HiFi Sequencing
- Wenger, Aaron (2021) Not All Long Reads Are Equal – High Accuracy Sets PacBio Apart
- Miller, David and Smith, Melissa Laird (2021) The Long and Short of Sequencing – Why HiFi Reads are the Future
- Becker, Aaron and Ekholm, Jenny and Harris, Charlotte and Kingham, Brewster and Vinnere Pettersson, Olga (2021) SMRT Sequencing as a Service – How to Bring Long-Read Technology to Your Core Lab
- Korlach, Jonas (2021) AGBT Presentation: Increasing the Solve Rate of Rare and Undiagnosed Genetic Diseases with HiFi Sequencing
- Wang, Bo (2021) PagBio Day: Comparative Genomic Analysis in Sorghum Highlights the Extent of Structural Variations and Sugarcane Aphid Resistance Genes
- Vierra, Michelle and Lewin, Haris (2021) PagBio Day: New Discoveries in Plant and Animal Sciences
- Schuele, Birgitt (2020) Long-read Sequencing and Optical Mapping of ATXN10 Repeat Expansion
- Holstege, Henne (2020) Uncovering Neurological Disorders Through an Examination of VNTRs
- Levandoski, Michael (2020) Webinar: Geographic and Temporal Mapping of the SARS-CoV-2 Pandemic in the United States
- (2020) Application Tutorial: Introduction to Variant Detection with HiFi Reads
- SMRT Sequencing Brochure: Delivering highly accurate long reads to drive discovery in life science (2021)
- Application Brief: Metagenomic sequencing with HiFi reads – Best Practices (2021)
- Publication at a Glance: The complete sequence of a human genome (2021)
- Informational Guide: Whole genome sequencing for understanding rare diseases (2021)
- Application Brief: Variant detection using whole genome sequencing with HiFi reads – Best Practices (2021)
- Application Brief: Whole genome sequencing for de novo assembly – Best Practices (2021)
- Application Brochure: Scalable human whole genome HiFi sequencing for rare and inherited disease research (2021)
- Core Lab Brochure: The most trusted long-read technology (2021)
- Application Brochure: Gene editing validation with HiFi reads (2021)
- Application Brief: No-Amp targeted sequencing – Best Practices (2020)
- Product Brochure: Sequel IIe System – Sequencing evolved (2020)
- Informational Guide: Understanding accuracy in DNA sequencing (2020)
- Application Note: Considerations for using the low and ultra-low DNA input workflows for whole genome sequencing (2020)
- Application Brochure: HiFi reads for highly accurate long-read sequencing (2020)
- Technical Note: Preparing DNA for PacBio HiFi sequencing – Extraction and quality control (2020)
- Informational Guide: Looking beyond the single reference genome to a pangenome for every species (2020)
- Infographic: A Genome Fit for a Giant – Sequencing the California redwood (2020)
- Application Brief: Targeted sequencing for amplicons – Best Practices (2019)
- Application Brief: Long-read RNA sequencing – Best Practices (2019)
- Sequel II System Brochure: Delivering highly accurate long reads (2019)
- Infographic: SMRT Sequencing – How it works (2019)