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De Novo Assembly

Generate finished genome assemblies with the PacBio RS II

Faster and more cost-effective DNA sequencing technologies are accelerating investigations of a broad range of genomes – from model organisms to pathogens that may have a direct impact on human health. However, only a limited number of species have been completely sequenced due to the inherent limitations of second-generation sequencing technologies, including GC-bias and the inability to resolve large structural variations. A complete genome is needed to fully understand the biological relevance of an organism.

The complexity of genome assembly is driven by a variety of factors, including the length and number of total fragments and the presence of repeat regions. The PacBio RS II single-molecule, real-time sequencing system provides extra-long read lengths that simplify and improve genome assembly. By reducing the number of contigs and producing superior consensus accuracy, researchers can finish genomes at a lower cost and with higher quality data.

Benefits:

  • Highest N50
  • Fewest contigs
  • Detect structural variation
  • 99.999% accuracy
  • Genome finishing at 1/10th the cost

  • Virtual Poster: De Novo Microbial Sequencing with Hybrid PacBio Genome Assemblies, Lawrence Hon (Pacific Biosciences)
  • Virtual Poster: Hybrid Assembly of a Nocturnal Lemur, Chris Mason (Weill Cornell Medical College)
  • Virtual Poster: Hybrid Assembly of Novel Bacterial Genomes, Ali Bashir (Mt. Sinai)
  • Virtual Poster: Understanding Single Molecule Accuracy, John Eid (Pacific Biosciences)
  • Virtual Poster: Upgrading Reference Genomes with PacBio Long Read Sequencing, Adam English (Baylor)
  • Webinar: Applications of SMRT Technology to Livestock Research, Timothy Smith (USDA)
  • Webinar: Automated, Non-Hybrid De Novo Genome Assemblies and Epigenomes of Bacterial Pathogens, Jonas Korlach (Pacific Biosciences)
  • Webinar: De-Novo Assembly of a Vertebrate Genome using PacBio Hybrids with Other Sequencing Technologies, Erich Jarvis (Duke University)
  • Webinar: Error Correction and De Novo Assembly of Complex Genomes, Mike Schatz (CSHL).
  • Webinar: Hybrid Error Correction and De Novo Assembly of Single-Molecule Sequencing Reads, Adam Phillippy & Sergey Koren (NBACC)
  • Webinar: Revealing the Genome through SMRT Biology, Kerstin Stangier (GATC Biotech)
  • Webinar: Using PacBio Reads and PBJelly Software to Improve Genomes: A Cost-Effective Approach to Finishing, Kim Worley (Baylor College of Medicine)
  • Brochure: PacBio RS II Sequencing System
  • Case Study: For Antarctic Genome, Scientists Find Unique Capability in SMRT DNA Sequencing
  • Case Study: The Next Frontier in Assembly – Long Reads Offer Finished Genomes
  • Perspective: Understanding Accuracy in SMRT Sequencing
  • Presentation: Hybrid Error Correction and De Novo Assembly of Single-molecule Sequencing Reads
  • Presentation: De Novo Assembly of Complex Crop Genomes, Mike Schatz, Cold Spring Harbor Laboratory
  • Presentation: The Best of Both Worlds: Combining PacBio with Short Read Technology for Improved de novo Genome Assembly
  • Primer: The Value of Finished Bacterial Genomes
  • Technical Note: De Novo and Hybrid Assembly
  • Technical Note: Experimental Design for De Novo Assembly
  • Technical Note: Microbial Analysis E. coli Genome Assembly
  • Technical Note: Shearing Large Insert Genomic DNA Rapidly using Covaris g-TUBEs
  • White Paper: Microbial Pathogen Identification and Characterization with the PacBio RS System
  • Poster: A Comparison of Microbial De Novo Assemblies Utilizing Long Read Sequencing Data, Lawrence Hon (Pacific Biosciences)
  • Poster: Automated, Non-Hybrid De Novo Genome Assemblies and Epigenomes of Bacterial Pathogens, Tyson Clark (Pacific Biosciences)
  • Poster: Combining Short (Illumina) and Long (PacBio) NGS Reads to Improve de novo Genome Assemblies of Rice and Saccharomyces Cerevisiae Genomes, Mike Schatz (Cold Spring Harbor Laboratory)
  • Poster: Genome Sequence and Hybrid Assembly of the Aye-Aye, a Nocturnal Lemur from Madagascar, Chris Mason (Weill Cornell Medical College)
  • Poster: Genome Sequencing of Endosymbiotic Bacteria Streptomyces sp. From Antarctic Lichen using SMRT Technology, Sujin Kim (DNA Link)
  • Poster: Genome Sequencing of Microbial Genomes using Single Molecule Real-Time Sequencing Technology, Sujin Kim (DNA Link)
  • Poster: Greater than 10 kb Read Lengths Routine when Sequencing with Pacific Biosciences' XL Release, Cheryl Heiner (Pacific Biosciences)
  • Poster: High Throughput Long Read DNA Sequencing using the PacBio RS, Yi Han (Baylor College of Medicine)
  • Poster: Hybrid Assembly of Bacterial Genomes, Ali Bashir (Mt. Sinai)
  • Poster: Mind the Gap - Upgrading Reference Genomes with Long Read Sequencing, Adam English (Baylor)
  • Poster: Minding the Gaps in the Arabidopsis Genome, Mitch Sudkamp (Monsanto Company)
  • Poster: Sequencing and De Novo Assembly of the 17q21.31 Disease-associated Region using Long Reads Generated by SMRT Sequencing Technology, Swati Ranade (Pacific Biosciences)
  • Poster: Taking Advantage of Long Read Lengths with Improved Library Preparation Methods, Joan Wilson (Pacific Biosciences)
  • Poster: Towards Finishing Genome Assembly Using SMRT Sequencing, Jenny Gu (Pacific Biosciences)
  • Poster: Utilizing Single Molecule Accuracy, John Eid (Pacific Biosciences)