Building Better Genomes.
Enabling Breakthrough Discovery.
PacBio HiFi reads provide an optimal balance between long read lengths (up to 25 kb) and high accuracy (>99%), generating contiguous, complete, and correct de novo assemblies.
The 2020 Plant and Animal Sciences SMRT Grant Program is Now Open!
Workflows: From DNA to Reference-Quality Genome Assembly with HiFi Sequencing
PacBio is the only sequencing technology to offer highly accurate long reads (HiFi reads).
|Use this workflow to generate high-quality de novo assemblies quickly and affordably.|
See the Complete Workflow
|Starting with unamplified genomic DNA, prepare libraries for whole genome sequencing using standardized protocols and workflow recommendations.|
- Start with >15 µg of unamplified genomic DNA
- Prepare a library in ~5 hours with the SMRTbell Express Template Prep Kit 2.0
- Enrich for 15-20 kb inserts with BluePippin size selection system
|The Sequel II System provides affordable HiFi coverage for high-quality genome assemblies.|
- Sequence using the circular consensus sequencing (CCS) mode
- Sequence up to a 2 Gb genome in a single SMRT Cell 8M*
- Run up to 200 samples (2 Gb) per year on a Sequel II System
- Coverage recommendations:
- 15-fold HiFi coverage for typical diploid genomes
- >20-fold HiFi coverage for repeat-rich genomes
*Read lengths, reads/data per SMRT Cell 8M and other sequencing performance results vary based on sample quality/type and insert size.
|Assemble genomes with full-solution analytical software tools and standard file formats.|
Studying Small-bodied Organisms?
Generate high-quality genome assemblies for single, wild-caught individuals from only ~300 ng of DNA.
Sequence Even the Smallest Organisms with Confidence
Contiguous, accurate insect genomes are essential tools to understand insect biology and to combat their role as disease vectors and agricultural pests. However, there are several key challenges to studying small-bodied organisms:
Due to their small size, many insects, including mosquitoes, provide only nanogram-level quantities of DNA.
It is common to pool many individuals to bolster DNA yield; however, this adds additional haplotypes and complicates the assembly process.
To reduce the negative effects of pooling individuals, the process of inbreeding for multiple generations is often necessary.
Solution: Low DNA Input Workflow – allows you to assemble high-quality genomes from a single, wild caught individual.
Explore how the low DNA input workflow is helping scientists answer questions about insect biology.
~ Kingan, S., et al. (2019) A high-quality de novo genome assembly from a single mosquito using PacBio sequencing. Genes, 10(1), 62.
Ready to study a small-bodied organism?
- Have access to a PacBio System? Try the low DNA input library preparation protocol.
- Want to do a low DNA input project at a service provider? Connect with a PacBio scientist.
Application Brief: Learn more about best practices for whole genome sequencing for de novo assembly
Get Your Project Started
To get a quote and get started on your genome project, contact one of our Certified Service Providers or a PacBio scientist. For information on acquiring a Sequel II System, please contact our sales team.
- Kingan, Sarah B et al. (2019) A high-quality genome assembly from a single, field-collected spotted lanternfly (Lycorma delicatula) using the PacBio Sequel II system GigaScience
- Tørresen, Ole K et al. (2019) Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases. Nucleic acids research
- He, Yaoxi et al. (2019) Long-read assembly of the Chinese rhesus macaque genome and identification of ape-specific structural variants. Nature communications
- Zhou, Yongfeng et al. (2019) The population genetics of structural variants in grapevine domestication. Nature plants
- Meier, Matthew J et al. (2019) Whole Genome Sequencing of the Mutamouse Model Reveals Strain- and Colony-Level Variation, and Genomic Features of the Transgene Integration Site. Scientific reports
- Wenger, Aaron M et al. (2019) Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nature biotechnology
- Liu, Qin et al. (2019) A chromosomal-level genome assembly for the insect vector for Chagas disease, Triatoma rubrofasciata. GigaScience
- Van de Weyer, Anna-Lena et al. (2019) A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana. Cell
- Bickhart, Derek M et al. (2019) Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation. Genome biology
- Jaworski, Coline C et al. (2019) Chromosome-level hybrid de novo genome assemblies as an attainable option for non-model organisms BioRxiv
- Low, Wai Yee et al. (2019) Haplotype-Resolved Cattle Genomes Provide Insights Into Structural Variation and Adaptation BioRxiv
- Yang, Zhaoen et al. (2019) Extensive intraspecific gene order and gene structural variations in upland cotton cultivars. Nature communications
- McCartney, Michael A. et al. (2019) The Genome of the Zebra Mussel, Dreissena polymorpha: A Resource for Invasive Species Research BioRxiv
- Zan, Jindong et al. (2019) A microbial factory for defensive kahalalides in a tripartite marine symbiosis. Science
- Warr, Amanda et al. (2019) An improved pig reference genome sequence to enable pig genetics and genomics research BioRxiv
- Chen, Zelin et al. (2019) De novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole-genome duplication. Science advances
- Yang, Ning et al. (2019) Genome assembly of a tropical maize inbred line provides insights into structural variation and crop improvement. Nature genetics
- Sánchez-Pérez, R et al. (2019) Mutation of a bHLH transcription factor allowed almond domestication. Science
- Yoshimura, Jun et al. (2019) Recompleting the Caenorhabditis elegans genome. Genome research
- Chang, Ching-Ho et al. (2019) Islands of retroelements are major components of Drosophila centromeres PLoS biology
- Zhuang, Weijian et al. (2019) The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication. Nature genetics
- Hotaling, Scott et al. (2019) The rising tide of high-quality genomic resources. Molecular ecology resources
- Kronenberg, Zev N. et al. (2019) Extended haplotype phasing of de novo genome assemblies with FALCON-Phase BioRxiv
- Ananthasayanam, Sudhakar et al. (2019) First near complete haplotype phased genome assembly of River buffalo (Bubalus bubalis) BioRxiv
- Chen, Wenbo et al. (2019) Genome sequence of the corn leaf aphid (Rhopalosiphum maidis Fitch). GigaScience
- Zhao, Dongyan et al. (2019) A chromosomal-scale genome assembly of Tectona grandis reveals the importance of tandem gene duplication and enables discovery of genes in natural product biosynthetic pathways. GigaScience
- Beaulaurier, John et al. (2019) Deciphering bacterial epigenomes using modern sequencing technologies. Nature reviews. Genetics
- Masonbrink, Rick et al. (2019) The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes. BMC genomics
- Kingan, Sarah et al. (2019) A high-quality de novo genome assembly from a single mosquito using PacBio sequencing Genes
- Laverty, Kaitlin U et al. (2019) A physical and genetic map of Cannabis sativa identifies extensive rearrangements at the THC/CBD acid synthase loci. Genome research
- Low, Wai Yee et al. (2019) Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity. Nature communications
- Ruan, Jue et al. (2019) Fast and accurate long-read assembly with wtdbg2 BioRxiv
- Hoff, Siv Nam Khang et al. (2019) Long-read sequence capture of the haemoglobin gene clusters across codfish species. Molecular ecology resources
- Formenti, Giulio et al. (2019) SMRT long reads and Direct Label and Stain optical maps allow the generation of a high-quality genome assembly for the European barn swallow (Hirundo rustica rustica). GigaScience
- Bell, Zachary W et al. (2019) Urotensin-related gene transcripts mark developmental emergence of the male forebrain vocal control system in songbirds. Scientific reports
- Poster: Baybayan, Primo et al. (2020) New advances in SMRT Sequencing facilitate multiplexing for de novo and structural variant studies
- 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: Vierra, M. et al. (2019) Structural variant detection in crops using low-fold coverage long-read sequencing
- Poster: Duncan, Turner et al. (2019) A low DNA input protocol for high-quality PacBio de novo genome assemblies
- Poster: Ekholm, Jenny et al. (2019) Streamlines SMRTbell library generation using addition-only, single tube strategy for all library types reduces time to results
- Poster: Baybayan, Primo et al. (2019) A high-quality de novo genome assembly from a single mosquito using PacBio sequencing
- Poster: Kingan, Sarah B. et al. (2019) A low DNA input protocol for high-quality PacBio de novo genome assemblies from single invertebrate individuals
- Poster: Peluso, Paul et al. (2019) Single molecule high-fidelity (HiFi) Sequencing with >10 kb libraries
- Poster: Blethrow, J. Sisneros, N. et al. (2018) Best practices for whole genome sequencing using the Sequel System
- Poster: Korlach, Jonas et al. (2018) High-quality de novo genome assembly and intra-individual mitochondrial instability in the critically endangered kakapo
- Poster: Heiner, Cheryl et al. (2018) Multiplexed complete microbial genomes on the Sequel System
- Poster: Vierra, Michelle et al. (2018) Characterizing the pan-genome of maize with PacBio SMRT Sequencing
- Poster: Concepion, C., et al. (2018) De novo assembly and preliminary annotation of the Schizocardium californicum genome
- Poster: Concepcion, G., et al. (2018) Structural variant detection in crops using PacBio SMRT Sequencing
- Poster: Kingan, Sarah et al. (2017) A high-quality genome assembly of SMRT sequences reveals long range haplotype structure in the diploid mosquito Aedes aegypti
- Poster: Korlach, Jonas et al. (2017) De novo PacBio long-read assembled avian genomes correct and add to genes important in neuroscience and conservation research
- Poster: Kingan, S. et al. (2017) A high-quality genome assembly of SMRT Sequences reveals long-range haplotype structure in the diploid mosquito Aedes aegypti
- Poster: Warr, A. et al. (2017) High-quality, highly contiguous re-assembly of the pig genome
- Poster: Concepcion, G. et al. (2017) Phased diploid genome assembly with single-molecule real-time sequencing
- Poster: Roach, M. et al. (2016) Assessing diversity and clonal variation of Australia’s grapevine germplasm: Curating the FALCON-Unzip Chardonnay de novo genome assembly
- Poster: Baybayan, Primo et al. (2016) Application specific barcoding strategies for SMRT Sequencing
- Poster: Ranade, Swati et al. (2016) Immune regions are no longer incomprehensible with SMRT Sequencing
- Poster: Seetin, Matthew et al. (2016) Long-read assembly of the Aedes aegypti Aag2 cell line genome resolves ancient endogenous viral elements
- Poster: Heiner, Cheryl et al. (2016) Low-input long-read sequencing for complete microbial genomes and metagenomic community analysis
- Poster: Chin, Jason et al. (2016) Un-zipping diploid genomes – revealing all kinds of heterozygous variants from comprehensive hapltotig assemblies
- Presentation: Chin, Jason et al. (2016) Diploid genome assembly and comprehensive haplotype sequence reconstruction
- Poster: Seetin, Matthew G et al. (2016) Long-read assembly of the Aedes aegypti Aag2 cell line genome resolves ancient endogenous viral elements
- Poster: Muehling, Jill R et al. (2016) SMRT Sequencing of the alala genome
- Poster: Lee, Hayan et al. (2015) The resurgence of reference quality genome
- Poster: Rank, David et al. (2015) Best practices for whole-genome de novo sequencing with long-read SMRT Sequencing.
- Presentation: Schatz, Michael et al. (2015) The resurgence of reference quality genome sequence.
- Presentation: VanBuren, Robert et al. (2015) De novo assembly of a complex panicoid grass genome using ultra-long PacBio reads with P6C4 chemistry
- Presentation: Strickler, Susan R et al. (2015) Genome assembly strategies of the recent polyploid, Coffea arabica.
- 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
- Korlach, Jonas and Graves-Lindsay, Tina and Vierra, Michelle (2020) PacBio Workshop: Understanding the biology of genomes with HiFi sequencing
- Schmutz, Jeremy and Conesa, Ana and Gharbi, Karim and Kuo, Richard (2020) Customer Experience: HiFi reads help scientists explore genomes and transcriptomes
- 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
- Mars, Kristin and Laird Smith, Melissa and Vinnere Pettersson, Olga and Hardigan, Michael (2020) Webinar: Sequencing 101 – How long-read sequencing improves access to genetic information
- Oppert, Brenda (2020) AGBT Presentation: Feed the World – Developing genomic resources for insects as food
- Blaxter, Mark (2020) PAG Conference: Endless forms: Genomes from the Darwin Tree of Life Project
- Vierra, Michelle (2020) PAG Conference: PacBio update on products and HiFi applications
- 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
- Bernberg, Erin (2019) User Group Meeting: Getting a read on one little worm with PacBio’s low DNA input workflow and the Agilent Femto Pulse System
- Korlach, Jonas (2019) User Group Meeting: Lowering input requirements
- Korlach, Jonas (2019) User Group Meeting: Sequencing chemistry & application updates
- Bernberg, Erin and Hotaling, Scott and Vierra, Michelle (2019) Webinar: Small Bodies, Big Genomes: Overcoming Large DNA Input Requirements for Long-Read Genome Assembly
- Kingan, Sarah and Carroll, Andrew (2019) Webinar: Variant calling and de novo genome assembly with PacBio HiFi reads
- Kingan, Sarah and McKernan, Kevin (2019) Webinar: Smoking out structural variants in the cannabis genome
- Korlach, Jonas and Garimella, Kiran and Tallon, Luke and McCarthy, Shane (2019) Webinar: Sequence with Confidence – Introducing the Sequel II System
- Fengler, Kevin (2019) PAG Conference: Dawn of the crop pangenome era
- Blethrow, Justin (2019) PAG Conference: How SMRT Sequencing is accelerating plant and animal genomics
- Clark, Andrew (2019) PAG Conference: Reference-quality drosophila genome assemblies for evolutionary analysis of previously inaccessible genomic regions
- Vernes, Sonia (2019) PAG Conference: The Bat1K project: bat genome, biology and implications
- Korlach, Jonas and Corney, Dave (2018) Webinar: A new paradigm in DNA sequencing – Highly accurate single-molecule long reads
- Block, Barbara and Peluso, Paul (2018) Webinar: Assembling high-quality genomes to solve nature’s mysteries
- Smith, Tim (2018) User Group Meeting: Application of genome assembly in Bovinae species
- Korlach, Jonas (2018) User Group Meeting: Low-input workflow for PacBio de novo genome assemblies
- (2018) Educational Video: Step 1 – from sample to sequencing data for de novo assembly
- (2018) Educational Video: Step 2 – de novo assembly of a genome
- Pillai, Nisha (2018) Webinar: A sketch of assembly recipes for PacBio data
- Ballard, Bill (2018) PAG Conference: Domestication: through the canines of a dingo
- Renner, Tanya (2018) PAG Conference: Long-read sequencing reveals complex genomic architecture in independent carnivorous plant lineages
- Williams, John (2018) PAG Conference: Using cattle subspecies crosses to explore chromosome of origin expression through Iso-seq analysis
- Hatas, Emily (2017) Webinar: SMRT Sequencing applications in plant and animal sciences: an overview
- Turner, Stephen (2017) Webinar: An introduction to PacBio’s long-read sequencing & how it has been used to make important scientific discoveries
- Sedlazeck, Fritz (2017) AGBT Virtual Poster: Quantifying the impact of improved genome assemblies on functional genomics
- Technical Note: Preparing DNA for PacBio HiFi sequencing – Extraction and quality control (2020)
- Application Brochure: HiFi reads for highly accurate long-read sequencing (2020)
- Infographic: A Genome Fit for a Giant – Sequencing the California redwood (2020)
- Application Brochure: What can you do with one SMRT Cell? (2020)
- Application Brief: Structural variant detection using whole genome sequencing – Best Practices (2020)
- PacBio Certified Service Providers (2020)
- Application Brief: Whole genome sequencing for de novo assembly – Best Practices (2019)
- Case Study: Diving Deep – Revealing the mysteries of marine life with SMRT Sequencing (2019)
- SMRT Sequencing Brochure: Delivering highly accurate long reads to drive discovery in life science (2019)
- Application Note: Low DNA input workflow considerations for de novo genome assembly (2019)
- Product Note: SMRTbell express template prep 2.0 for large-insert libraries (2019)
- Infographic: Gold-standard reference genomes accelerate science (2018)
- De Novo Assembly Brochure: Assembly options for your SMRT Sequencing data (2018)
- Technical Note: Preparing samples for PacBio whole genome sequencing for de novo assembly – Collection and storage (2018)
- Case Study: Pioneering a pan-genome reference collection (2018)
- Case Study: PacBio and Dovetail – For cashew genome, combining technologies yields chromosome-scale assembly (2017)
- Case Study: Breeding a better Cabernet – SMRT Sequencing provides detailed view of grape genome (2016)
- Case Study: First comprehensive view of maize genome reveals regulatory and structural mechanisms (2016)