Advance genomics with long-read sequencing, enabled by Single Molecule, Real-Time (SMRT) Sequencing
SMRT Sequencing is built upon two key innovations: zero-mode waveguides (ZMWs) and phospholinked nucleotides. ZMWs allow light to illuminate only the bottom of a well in which a DNA polymerase/template complex is immobilized. Phospholinked nucleotides allow observation of the immobilized complex as the DNA polymerase produces a completely natural DNA strand.
The SMRT Sequencing advantages
SMRT Sequencing is ideal for a variety of research applications and offers many benefits, including:
- Longest average read lengths
- Highest consensus accuracy
- Uniform coverage
- Simultaneous epigenetic characterization
- Single-molecule resolution
Selected Resources
- Callahan, Benjamin J et al. (2019) High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution. Nucleic acids research
- Zhang, Xiujuan et al. (2019) Full-length transcriptome analysis of Litopenaeus vannamei reveals transcript variants involved in the innate immune system. Fish & shellfish immunology
- Wenger, Aaron M et al. (2019) Highly-accurate long-read sequencing improves variant detection and assembly of a human genome BioRxiv
- Kumari, Romika et al. (2018) PausePred and Rfeet: webtools for inferring ribosome pauses and visualizing footprint density from ribosome profiling data. RNA
- Kosicki, Michael et al. (2018) Repair of double-strand breaks induced by CRISPR-Cas9 leads to large deletions and complex rearrangements. Nature biotechnology
- Tai, Phillip WL et al. (2018) Adeno-associated virus genome population sequencing achieves full vector genome resolution and reveals human-vector chimeras Molecular therapy
- Sedlazeck, Fritz J et al. (2018) Accurate detection of complex structural variations using single-molecule sequencing. 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
- Ardui, Simon et al. (2018) Detecting AGG interruptions in females with a FMR1 premutation by long-read Single-Molecule Sequencing: A 1 year clinical experience. Frontiers in 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
- Hebert, Paul D N et al. (2018) A Sequel to Sanger: amplicon sequencing that scales. BMC genomics
- Ardui, Simon et al. (2018) Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics. Nucleic acids research
- Hobbs, Matthew et al. (2017) Long-read genome sequence assembly provides insight into ongoing retroviral invasion of the koala germline. Scientific reports
- Wang, Yuan et al. (2017) Profiling of oral microbiota in early childhood caries using Single-Molecule Real-Time Sequencing Frontiers in microbiology
- Semler, Matthew R et al. (2017) Novel full-length major histocompatibility complex class I allele discovery and haplotype definition in pig-tailed macaques. Immunogenetics
- Bao, Jiandong et al. (2017) PacBio sequencing reveals transposable element as a key contributor to genomic plasticity and virulence variation in Magnaporthe oryzae. Molecular plant
- Teng, Jade LL et al. (2017) PacBio but not Illumina technology can achieve fast, accurate and complete closure of the high GC, complex Burkholderia pseudomallei two-chromosome genome Frontiers in microbiology
- Costa, Stephen K et al. (2017) Bypassing the Restriction System To Improve Transformation of Staphylococcus epidermidis. Journal of bacteriology
- Borràs, Daniel M et al. (2017) Detecting PKD1 variants in polycystic kidney disease patients by single-molecule long-read sequencing. Human mutation
- Merker, Jason D et al. (2017) Long-read genome sequencing identifies causal structural variation in a Mendelian disease. Genetics in medicine
- Pasini, Erica M et al. (2017) An improved Plasmodium cynomolgi genome assembly reveals an unexpected methyltransferase gene expansion. Wellcome open research
- Pootakham, Wirulda et al. (2017) High resolution profiling of coral-associated bacterial communities using full-length 16S rRNA sequence data from PacBio SMRT sequencing system. Scientific reports
- Jiao, Yinping et al. (2017) Improved maize reference genome with single-molecule technologies. Nature
- Roe, D. et al. (2017) Revealing complete complex KIR haplotypes phased by long-read sequencing technology Genes and immunity
- Minio, Andrea et al. (2017) How Single Molecule Real-Time Sequencing and haplotype phasing have enabled reference-grade diploid genome assembly of wine grapes. Frontiers in plant science
- Yue, Jia-Xing et al. (2017) Contrasting evolutionary genome dynamics between domesticated and wild yeasts. Nature genetics
- Elghraoui, Afif et al. (2017) SMRT genome assembly corrects reference errors, resolving the genetic basis of virulence in Mycobacterium tuberculosis. BMC genomics
- Motooka, Daisuke et al. (2017) Fungal ITS1 deep-sequencing strategies to reconstruct the composition of a 26-species community and evaluation of the gut mycobiota of healthy Japanese individuals. Frontiers in microbiology
- Potapov, Vladimir et al. (2017) Examining sources of error in PCR by single-molecule sequencing. PloS one
- He, Susu et al. (2016) Mechanisms of evolution in high-consequence drug resistance plasmids. mBio
- Suzuki, Yuta et al. (2016) AgIn: Measuring the landscape of CpG methylation of individual repetitive elements. Bioinformatics
- Vembar, Shruthi Sridhar et al. (2016) Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome through long-read (>11?kb), single molecule, real-time sequencing. DNA research
- Bellec, Arnaud et al. (2016) Long read sequencing technology to solve complex genomic regions assembly in plants Journal of next generation sequencing & applications
- Poster: Larrea, Andres et al. (2018) A simple segue from Sanger to high-throughput SMRT Sequencing with a M13 barcoding system
- Poster: Kingan, Sarah et al. (2018) FALCON-Phase integrates PacBio and HiC data for de novo assembly, scaffolding and phasing of a diploid Puerto Rican genome (HG00733)
- Poster: Ekholm, J. et al. (2018) Amplification-free, CRISPR-Cas9 targeted enrichment and SMRT Sequencing of repeat-expansion disease causative genomic regions
- Poster: Ranade, S. et al. (2018) High-throughput SMRT Sequencing of clinically relevant targets
- Poster: Liqing, Tian et al. (2018) Allelic specificity of immunoglobulin heavy chain (IGH@) translocation in B-cell acute lymphoblastic leukemia (B-ALL) unveiled by long-read sequencing
- Poster: Clark, Tyson A. et al. (2018) Amplification-free targeted enrichment and SMRT Sequencing of repeat-expansion genomic regions
- Poster: Korlach, Jonas et al. (2018) High-quality de novo genome assembly and intra-individual mitochondrial instability in the critically endangered kakapo
- Poster: Chakraborty, Shreyasee et al. (2018) Mitochondrial DNA sequencing using PacBio SMRT technology
- Poster: Concepion, C., et al. (2018) De novo assembly and preliminary annotation of the Schizocardium californicum genome
- Poster: Tseng, E., et al. (2018) Haplotyping of full-length transcript reads from long-read sequencing can reveal allelic imbalances in isoform expression
- Poster: Concepcion, G., et al. (2018) Structural variant detection in crops using PacBio SMRT Sequencing
- Poster: McLaughlin, I., et al. (2017) Targeted sequencing using a long-read sequencing technology
- Poster: Kingan, S. et al. (2017) Structural variant detection with low-coverage PacBio sequencing
- Poster: Baybayan, P. et al. (2017) Detection of low-frequency somatic variants using Single-Molecule, Real-Time Sequencing
- Poster: Oh, Steve et al. (2017) T-cell receptor profiling using PacBio sequencing of SMARTer libraries
- Poster: McCalmon, S. et al. (2016) “SMRTer Confirmation”: Scalable clinical read-through variant confirmation using the Pacific Biosciences SMRT Sequencing platform
- Poster: Ekholm, J. et al. (2016) Enrichment of unamplified DNA and long-read SMRT Sequencing to unlock repeat expansion disorders
- Poster: Laird Smith, M. et al. (2016) An improved circular consensus algorithm with an application to detect HIV-1 Drug Resistance Associated Mutations (DRAMs)
- Poster: Heiner, C. et al. (2016) WGS SMRT Sequencing of patient samples from a fecal microbiota transplant trial
- Poster: Sethuraman, Anand et al. (2016) Highly sensitive and cost-effective detection of somatic cancer variants using single-molecule, real-time sequencing
- Poster: Hepler, N. Lance et al. (2016) An improved circular consensus algorithm with an application to detection of HIV-1 Drug-Resistance Associated Mutations (DRAMs)
- Poster: Seetin, Matthew G et al. (2016) Long-read assembly of the Aedes aegypti Aag2 cell line genome resolves ancient endogenous viral elements
- Poster: Sethuraman, Anand et al. (2015) Analysis of full-length metagenomic 16S genes by Single Molecule, Real-Time Sequencing
- Poster: Hall, Richard J. et al. (2015) Profiling metagenomic communities using circular consensus and Single Molecule, Real-Time Sequencing.
- Poster: Hall, Richard J. et al. (2015) Assembly of complete KIR haplotypes from a diploid individual by the direct sequencing of full-length fosmids.
- Poster: Brown, Michael et al. (2015) High-accuracy, single-base resolution of near-full-length HIV genomes.
- Presentation: Schatz, Michael et al. (2015) The resurgence of reference quality genome sequence.
- Korlach, Jonas and Corney, Dave (2018) Webinar: A new paradigm in DNA sequencing – Highly accurate single-molecule long reads
- Ameur, A. and Graves-Lindsay, T. and Peluso, P. (2018) Webinar: Assembling high-quality human reference genomes for global populations
- Hoischen, A. and Wenger, A (2018) Webinar: Sequencing structural variants for disease gene discovery and population genetics
- Williams, John (2018) PAG Conference: Using cattle subspecies crosses to explore chromosome of origin expression through Iso-seq analysis
- Ranade, Swati (2017) Webinar: A paradigm shift in HLA sequencing: from exons to high-resolution allele-level HLA yyping
- Korlach, Jonas (2017) Webinar: Addressing “NGS Dead Zones” with third generation PacBio sequencing
- Ashby, Meredith (2017) Webinar: Chasing alternative splicing in cancer: Simplified full-length isoform sequencing
- Turner, Stephen (2017) Webinar: An introduction to PacBio’s long-read sequencing & how it has been used to make important scientific discoveries
- Cereb, Nezih (2017) AGBT PacBio Workshop: High-throughput HLA class I whole gene and HLA class II long range typing on PacBio RSII and Sequel Platforms
- Ameur, Adam (2017) AGBT Virtual Poster: Analysis method for amplification-free SMRT sequencing and assessment on repeat expansions in Huntington’s disease
- Sedlazeck, Fritz (2017) AGBT Virtual Poster: Quantifying the impact of improved genome assemblies on functional genomics
- Paulin, Lars (2017) AGBT Virtual Poster: Single-molecule sequencing reveals the presence of distinct JC polyomavirus populations in patients with progressive multifocal leukoencephalopathy
- Jarvis, Erich (2017) PAG PacBio Workshop: Comparative analyses of next generation technologies for generating chromosome-level reference genome assemblies
- Ashley, Euan (2016) ASHG PacBio Workshop: Towards precision medicine
- Wenger, Aaron (2016) Video: Using the Integrative Genomics Viewer (IGV) to visualize PacBio long-read SMRT Sequencing data
- Paxinos, Ellen (2016) AGBT Virtual Poster: An improved circular consensus algorithm with an application to detect HIV-1 Drug Resistance Associated Mutations (DRAMs)
- Heiner, Cheryl (2016) AGBT Virtual Poster: Low-input long-read sequencing for complete microbial genomes and metagenomic community analysis
- Hall, Richard (2016) AGBT Virtual Poster: Profiling the microbiome in fecal microbiota transplantation using circular consensus and Single Molecule, Real-Time Sequencing
- Morey, Robert (2016) AGBT Virtual Poster: Using PacBio sequencing as a synthetic biology error analysis tool
- Ware, Doreen (2016) PAG PacBio Workshop: A-maize-ing time for plant science – SMRT Sequencing of the maize genome and transcriptome
- Ryder, Oliver (2016) PAG PacBio Workshop: Conservation genomics of a critically endangered Hawaiian bird: A high quality genome assembly of the ‘alala will assist in population management and reintroduction
- Gyllensten, Ulf (2015) AGBT Virtual Poster: Clinical sequencing using Pacific Biosciences RS II for HLA typing and monitoring of drug resistance in chronic myeloid leukemia (CML)
- Application Brief: Microbial whole genome sequencing – Best Practices (2019)
- Case Study: Mining complex metagenomes for protein discovery with long-read sequencing (2019)
- Case Study: Sequencing an historic bacterial collection for the future (2019)
- SMRT Sequencing Brochure: Delivering highly accurate long reads to drive discovery in life science (2019)
- Application Brief: Targeted sequencing for amplicons – Best Practices (2018)
- Infographic: Gold-standard reference genomes accelerate science (2018)
- De Novo Assembly Brochure: Assembly options for your SMRT Sequencing data (2018)
- Case Study: Pioneering a pan-genome reference collection (2018)
- Whitepaper: Structural variation in the human genome (2017)
- Case Study: SMRT sequencing brings clarity to HIV vaccine and transplant research at the Wisconsin national primate research center (2017)
- Case Study: Improving precision medicine studies in Asia using ethnicity-specific human reference genomes and PacBio long-read sequencing (2017)
- Case Study: Breeding a better Cabernet – SMRT Sequencing provides detailed view of grape genome (2016)
- Case Study: Scientists deconstruct cancer complexity through genome and transcriptome analysis (2016)