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.
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.
Read the Blog Post to Learn More
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
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.
2020 Microbial Genomics SMRT Grant Program – Now Open
Explore the Microbial World in High Resolution
Apply by November 6, 2020 for your chance to win free SMRT Sequencing
How to Get Started with HiFi Sequencing?
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Learn more about HiFi sequencing using the award-winning Sequel II System
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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: 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
- Chakraborty, Shreyasee and Eng, Kevin and Warner, Sarah and Lee, Walter and Madamba, Nicole and Obermoeller, Dawn and Wenger, Aaron and Weiand, Michael and Larrea, Andres and Baybayan, Primo (2020) Video Poster: High-throughput HiFi library workflow for human whole genome sequencing on the Sequel II System
- Wenger, Aaron (2020) Educational Video: Variant Detection with HiFi Reads – Understanding Results from the precisionFDA Truth Challenge
- Geib, Scott and Laumer, Christopher and Uliano da Silva, Marcela and Vierra, Michelle (2020) Webinar: No Organism Too Small – Build high-quality genome assemblies of small organisms with HiFi sequencing
- Ameur, Adam (2020) Webinar: SMRT Sequencing applications for human genomics and medicine
- Sund, Kristen and Wenger, Aaron (2020) Webinar: Increasing solve rates for rare and Mendelian diseases with long-read sequencing
- Ashby, Meredith and Laird-Smith, Melissa and Watson, Corey (2020) Webinar: Understanding SARS-CoV-2 and host immune response to COVID-19 with PacBio sequencing
- Korlach, Jonas and Graves-Lindsay, Tina and Vierra, Michelle (2020) PacBio Workshop: Understanding the biology of genomes with HiFi sequencing
- Kuo, Richard (2020) Customer Experience: A new view of non-coding RNA with PacBio HiFi reads
- Gharbi, Karim (2020) Customer Experience: Advancing UK genomics research with the PacBio Sequel II System
- Schmutz, Jeremy and Conesa, Ana and Gharbi, Karim and Kuo, Richard (2020) Customer Experience: HiFi reads help scientists explore genomes and transcriptomes
- Conesa, Ana (2020) Customer Experience: Improving transcriptome research with PacBio HiFi reads
- Schmutz, Jeremy (2020) Customer Experience: PacBio HiFi reads improve genome sequencing at HudsonAlpha
- Korlach, Jonas (2020) Webinar: Long HiFi reads for high-quality genome assemblies
- Ashby, Meredith (2020) Webinar: Opportunities for using PacBio Long-read sequencing for COVID-19 research
- Weber, Kay (2020) Webinar: Bioinformatics lunch & learn – HiFi assembly
- Oppert, Brenda (2020) AGBT Presentation: Feed the World – Developing genomic resources for insects as food
- Graves-Lindsay, Tina (2020) AGBT Presentation: Generating high quality human reference assemblies with PacBio sequencing
- Ameur, Adam (2020) AGBT Presentation: Studying CRISPR guide RNA specificity by amplification-free long-read sequencing
- (2020) Video: Introduction to PacBio highly accurate long-read sequencing
- Vierra, Michelle (2020) PAG Conference: PacBio update on products and HiFi applications
- U’Ren, Jana (2020) PAG Conference: Phylogenetic insights into the endophyte symbiosis using PacBio ribosomal DNA sequencing
- Nijland, Bart (2020) PAG Conference: The impact of highly accurate PacBio sequence data on the assembly of a tetraploid rose
- Korlach, Jonas (2020) PAG Conference: Workshop introduction
- Ashby, Meredith and Eversole, Kelley (2019) Webinar: Unbiased, efficient characterization of metagenome functions with PacBio HiFi sequencing
- Hatas, Emily (2019) ASHG PacBio Workshop: Sequence with confidence – A new era of highly accurate long-read sequencing
- Vollger, Mitchell (2019) User Group Meeting: Improved assembly of segmental duplications using HiFi
- Mars, Kristin (2019) User Group Meeting: No Assembly Required – Making the most of Iso-Seq data
- Korlach, Jonas (2019) User Group Meeting: Sequencing chemistry & application updates
- Ashby, Meredith (2019) User Group Meeting: Unbiased characterization of metagenome composition and function using HiFi sequencing on the PacBio Sequel II System
- Kingan, Sarah and Carroll, Andrew (2019) Webinar: Variant calling and de novo genome assembly with PacBio HiFi reads
- Korlach, Jonas and Garimella, Kiran and Tallon, Luke and McCarthy, Shane (2019) Webinar: Sequence with Confidence – Introducing the Sequel II System
- Hunkapiller, Michael (2019) AGBT Presentation: HiFi long reads for comprehensive genomic analysis
- Badgett, Marty (2019) AGBT Presentation: The Sequel II System – The next evolution of SMRT Sequencing
- Aro, Lori and Heiner, Cheryl (2019) Webinar: Amplicon sequencing with confidence – High-fidelity, long-read PacBio sequencing solutions
- 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)
- Core Lab Brochure: The most trusted long-read technology (2020)
- Infographic: A Genome Fit for a Giant – Sequencing the California redwood (2020)
- Application Brief: Metagenomic sequencing with HiFi reads – Best Practices (2020)
- Application Brief: Whole genome sequencing for de novo assembly – Best Practices (2019)
- SMRT Sequencing Brochure: Delivering highly accurate long reads to drive discovery in life science (2019)
- Application Brief: Variant detection using whole genome sequencing with HiFi reads – Best Practices (2019)
- Application Brief: No-Amp targeted sequencing – Best Practices (2019)
- 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)