Building Better Genomes.
Enabling Breakthrough Discovery.
With megabase-size contig N50s, consensus accuracies >99%, and tools for phasing haplotypes, using PacBio long reads for de novo assembly of plant and animal genomes captures undetected SNVs, fully intact genes, and regulatory regions embedded in complex structures that fragmented draft genomes often miss.
Explore the resources below for tips, tricks, and best practices at each step in the whole genome sequencing workflow for generating high-quality genome assemblies using Single Molecule, Real-Time (SMRT) Sequencing data.
 | Sample, DNA, and Library Prep |
| Ensure the high quality of your sample and DNA to generate the optimal library with our technical notes and video tutorials. |
 | Sequencing |
| Scale coverage based on your project needs and achieve up to 12 Gb of sequence data per SMRT Cell on the Sequel System following our best practices guide. |
 | Genome Assembly and Polishing |
| Assemble a genome at the push of a button or with customizable command line analytical software tools with the help of our bioinformatics guide to de novo assembly and video tutorials. |
 | Genome Annotation |
| Make direct, imputation-free genome annotations with our long-read RNA sequencing solution, the Iso-Seq method. |
Genome Assembly Project Builder
Explore our project builder for planning de novo assembly projects and receive tailored recommendations for each step in the workflow from sample prep to assembly and annotation.
To get a quote and get started on your genome project, contact one of our Certified Service Providers located across the globe for fast, convenient SMRT Sequencing. For information on acquiring a Sequel System, please contact our world-class sales team.
Selected Resources
- Koren, Sergey et al. (2018) De novo assembly of haplotype-resolved genomes with trio binning. Nature biotechnology
- Fallon, Timothy R et al. (2018) Firefly genomes illuminate parallel origins of bioluminescence in beetles. eLife
- Tran, Hue T M et al. (2018) Use of a draft genome of coffee (Coffea arabica) to identify SNPs associated with caffeine content. Plant biotechnology journal
- Gong, Gaorui et al. (2018) Chromosomal-level assembly of yellow catfish genome using third-generation DNA sequencing and Hi-C analysis. GigaScience
- Sun, Silong et al. (2018) Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes. Nature genetics
- Sutton, Jolene et al. (2018) A high-quality, long-read de novo genome assembly to aid conservation of Hawaii’s last remaining crow species Genes
- VanBuren, Robert et al. (2018) A near complete, chromosome-scale assembly of the black raspberry (Rubus occidentalis) genome. GigaScience
- Löber, Ulrike et al. (2018) Degradation and remobilization of endogenous retroviruses by recombination during the earliest stages of a germ-line invasion. Proceedings of the National Academy of Sciences of the United States of America
- Zhou, Chao et al. (2018) Identification and analysis of adenine N6-methylation sites in the rice genome. Nature plants
- Kumari, Romika et al. (2018) PausePred and Rfeet: webtools for inferring ribosome pauses and visualizing footprint density from ribosome profiling data. RNA
- Roach, Michael J. et al. (2018) Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay BioRxiv
- Poulter, Russell T. M. et al. (2018) Comparison between complete genomes of an isolate of Pseudomonas syringae pv. actinidiae from Japan and a New Zealand isolate of the pandemic. Scientific reports
- Johnson, Rebecca N et al. (2018) Adaptation and conservation insights from the koala genome. Nature genetics
- Li, Fay-Wei et al. (2018) Fern genomes elucidate land plant evolution and cyanobacterial symbioses. Nature plants
- Gao, Fei et al. (2018) Long-read sequencing and de novo genome assembly of Ammopiptanthus nanus, a desert shrub. GigaScience
- Marx, Vivien et al. (2018) What makes birds and bats the talk of the town. Nature methods
- Shields, Emily J et al. (2018) High-quality genome assemblies reveal long non-coding RNAs expressed in ant brains. Cell reports
- Kronenberg, Zev N et al. (2018) High-resolution comparative analysis of great ape genomes. Science
- Du, Xiongming et al. (2018) Resequencing of 243 diploid cotton accessions based on an updated A genome identifies the genetic basis of key agronomic traits. Nature genetics
- Raymond, Olivier et al. (2018) The Rosa genome provides new insights into the domestication of modern roses. Nature genetics
- Ling, Hong-Qing et al. (2018) Genome sequence of the progenitor of wheat A subgenome Triticum urartu. Nature
- Wang, Wensheng et al. (2018) Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature
- Harumoto, Toshiyuki et al. (2018) Male-killing toxin in a bacterial symbiont of Drosophila. Nature
- Xu, Qing et al. (2018) The genomic floral language of rose Nature genetics
- Zhao, Liang et al. (2018) The highly heterogeneous methylated genomes and diverse restriction-modification systems of bloom-forming Microcystis. Harmful algae
- Sedlazeck, Fritz J et al. (2018) Piercing the dark matter: bioinformatics of long-range sequencing and mapping. Nature reviews. Genetics
- Hu, Yi et al. (2018) Herbivorous turtle ants obtain essential nutrients from a conserved nitrogen-recycling gut microbiome. Nature communications
- Yadav, Vikas et al. (2018) RNAi is a critical determinant of centromere evolution in closely related fungi. Proceedings of the National Academy of Sciences of the United States of America
- Minio, Andrea et al. (2018) Isoform-scale annotation and expression profiling of the Cabernet Sauvignon transcriptome using single-molecule sequencing of full-length cDNA BioRxiv
- de Castro Nunes, Renata et al. (2018) Structure and distribution of centromeric retrotransposons at diploid and allotetraploid Coffea centromeric and pericentromeric regions. Frontiers in plant science
- Schwessinger, Benjamin et al. (2018) A near-complete haplotype-phased genome of the dikaryotic wheat stripe rust fungus Puccinia striiformis f. sp. tritici reveals high interhaplotype diversity. mBio
- Cheng, Yuanyuan et al. (2018) Characterisation of MHC class I genes in the koala. Immunogenetics
- Lu, You et al. (2018) Comparative genomic analyses of Clavibacter michiganensis subsp. insidiosus and pathogenicity on Medicago truncatula. Phytopathology
- Edger, Patrick P et al. (2018) Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity. GigaScience
- Nowoshilow, Sergej et al. (2018) The axolotl genome and the evolution of key tissue formation regulators. Nature
- 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.
- Presentation: Wing, Rod A et al. (2015) Old school/new school genome sequencing: One step backward — a quantum leap forward.
- Poster: Karalius, Joseph et al. (2015) Resources for advanced bioinformaticians working in plant and animal genomes with SMRT Sequencing.
- 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
- Jarvis, Erich (2017) PAG PacBio Workshop: Comparative analyses of next generation technologies for generating chromosome-level reference genome assemblies
- Johnson, Rebecca (2017) PAG PacBio Workshop: De novo sequencing of the koala genome
- Matthews, Ben (2017) PAG PacBio Workshop: Genome assembly and molecular genetics of the dengue, yellow fever, and zika vector Aedes aegypti
- Wing, Rod (2017) PAG PacBio Workshop: Introducing 5 new high-quality PacBio genome assemblies for rice to help solve the 10-billion people question
- Korlach, Jonas (2017) PAG PacBio Workshop: SMRT Sequencing for complete genomes
- PacBio Certified Service Providers (2018)
- Application Brief: Large genome whole genome sequencing – Best Practices (2018)
- SMRT Sequencing Brochure: Revolutionize genomics with SMRT Sequencing (2018)
- Infographic: Gold-standard reference genomes accelerate science (2018)
- De Novo Assembly Brochure: Assembly options for your SMRT Sequencing data (2018)
- Technical Note: Preparing libraries for PacBio whole genome sequencing for de novo assembly – Quality control and size selection (2018)
- Technical Note: Preparing DNA for PacBio whole genome sequencing for de novo assembly – Quality control and shearing (2018)
- Technical Note: Preparing samples for PacBio whole genome sequencing for de novo assembly – Collection and storage (2018)