Korean service provider DNA Link has established strong expertise with the PacBio sequencing platform in response to high global demand for the technology.
Single Molecule, Real-Time (SMRT) Sequencing uses the natural process of DNA replication to sequence long fragments of native DNA in order to produce highly accurate long reads, or HiFi reads. As such, starting with high-quality, high molecular weight (HMW) genomic DNA (gDNA) will result in longer libraries and better performance during sequencing. This technical note is intended to give recommendations, tips and tricks for the extraction of DNA, as well as assessing and preserving the quality and size of your DNA sample to be used for HiFi sequencing.
Interested to learn about pangenomes? Explore this guide to learn how they provide a more complete picture of the core genes of a given species and how that can provide better biological understanding.
Our understanding of microbiology has evolved enormously over the last 150 years. Few institutions have witnessed our collective progress more closely than the National Collection of Type Cultures (NCTC). In fact, the collection itself is a record of the many milestones microbiologists have crossed, building on the discoveries of those who came before. To date, 60% of NCTC’s historic collection now has a closed, finished reference genome, thanks to PacBio Single Molecule, Real- Time (SMRT) Sequencing. We are excited to be their partner in crossing this latest milestone on their quest to improve human and animal health by understanding the…
The bacteria living on and within us can impact health, disease, and even our behavior, but there is still much to learn about the breadth of their effects. The torrent of new discoveries unleashed by high-throughput sequencing has captured the imagination of scientists and the public alike. Scientists at Second Genome are hoping to apply these insights to improve human health, leveraging their bioinformatics expertise to mine bacterial communities for potential therapeutics. Recently they teamed up with scientists at PacBio to explore how long-read sequencing might supplement their short-read-based pipeline for gene discovery, using an environmental sample as a test…
Many scientists are using PacBio Single Molecule, Real-Time (SMRT) Sequencing to explore the genomes and transcriptomes of a wide variety of marine species and ecosystems. These studies are already adding to our understanding of how marine species adapt and evolve, contributing to conservation efforts, and informing how we can optimize food production through efficient aquaculture.
The UK’s National Collection of Type Cultures (NCTC) is a unique collection of more than 5,000 expertly preserved and authenticated bacterial cultures, many of historical significance. Founded in 1920, NCTC is the longest established collection of its type anywhere in the world, with a history of its own that has reflected — and contributed to — the evolution of microbiology for more than 100 years.
AGBT 2013 Presentation Slides: Cold Spring Harbor Laboratory’s Michael Schatz presented strategies for de novo assembly of crop genomes with PacBio technolgy.
Background: To better understand the relationships among HIV-1 viruses in linked transmission pairs, we sequenced several samples representing HIV transmission pairs from the Zambia Emory HIV Research Project (Lusaka, Zambia) using Single Molecule, Real-Time (SMRT) Sequencing. Methods: Single molecules were sequenced as full-length (9.6 kb) amplicons directly from PCR products without shearing. This resulted in multiple, fully-phased, complete HIV-1 genomes for each patient. We examined Single Genome Amplification (SGA) prepped samples, as well as samples containing complex mixtures of genomes. We detail mathematical techniques used in viral variant subspecies identification, including clustering distance metrics and mutual information, which were used…
Background: HIV-1 proviruses in peripheral blood mononuclear cells (PBMCs) are felt to be an important reservoir of HIV-1 infection. Given that this pool represents an archival library, it can be used to study virus evolution and CD4+ T cell survival. Accurate study of this pool is burdened by difficulties encountered in sequencing a full-length proviral genome, typically accomplished by assembling overlapping pieces and imputing the full genome. Methodology: Cryopreserved PBMCs collected from a total of 8 HIV+ patients from 1997-2001 were used for genomic DNA extraction. Patients had been receiving cART for 2-8 years at the time samples were obtained.…
Single Molecule, Real-Time (SMRT) Sequencing holds promise for addressing new frontiers in large genome complexities, such as long, highly repetitive, low-complexity regions and duplication events, and differentiating between transcript isoforms that are difficult to resolve with short-read technologies. We present solutions available for both reference genome improvement (>100 MB) and transcriptome research to best leverage long reads that have exceeded 20 Kb in length. Benefits for these applications are further realized with consistent use of size-selection of input sample using the BluePippin™ device from Sage Science. Highlights from our genome assembly projects using the latest P5-C3 chemistry on model organisms…
Advances in RNA sequencing have accelerated our understanding of the transcriptome, however isoform discovery remains challenging due to short read lengths. The Iso-Seq Application provides a new alternative to sequence full-length cDNA libraries using long reads from the PacBio RS II. Identification of long and often rare isoforms is demonstrated with rat heart and lung RNA prepared using the Clontech® SMARTer® cDNA preparation kit, followed by agarose-gel size selection in fractions of 1-2 kb, 2-3 kb and 3-6 kb. For each tissue, 1.8 and 1.2 million reads were obtained from 32 and 26 SMRT Cells, respectively. Filtering for reads with…
PacBio sequencing holds promise for addressing large-genome complexities, such as long, highly repetitive, low-complexity regions and duplication events that are difficult to resolve with short-read technologies. Several strategies, with varying outcomes, are available for de novo sequencing and assembling of larger genomes. Using a diploid fungal genome, estimated to be ~80 Mb in size, as the basis dataset for comparison, we highlight assembly options when using only PacBio sequencing or a combined strategy leveraging data sets from multiple sequencing technologies. Data generated from SMRT Sequencing was subjected to assembly using different large-genome assemblers, and comparisons of the results will be…
Third generation single molecule sequencing technology from Pacific Biosciences, Moleculo, Oxford Nanopore, and other companies are revolutionizing genomics by enabling the sequencing of long, individual molecules of DNA and RNA. One major advantage of these technologies over current short read sequencing is the ability to sequence much longer molecules, thousands or tens of thousands of nucleotides instead of mere hundreds. This capacity gives researchers substantially greater power to probe into microbial, plant, and animal genomes, but it remains unknown on how to best use these data. To answer this, we systematically evaluated the human genome and 25 other important genomes…