Asset Tag: Microbiology
September 24, 2021 |
Generation of Lineage-Resolved Complete Metagenome-Assembled Genomes in Complex Microbial Communities
In this SMRT Science Journal Club talk, Mikhail Kolmogorov from the University of California Santa Cruz discusses his computational approach to the generation of lineage-resolved complete MAGs by precision phasing.
September 7, 2021 |
Resolving Complex Pathogenic Alleles using HiFi Long-Range Amplicon Data and a New Clustering Algorithm
Many genetic diseases are mapped to structurally complex loci. These regions contain highly similar paralogous alleles (>99% identity) that span kilobases within the human genome. Comprehensive screening for pathogenic variants is incomplete and labor intensive using short-reads or optical mapping. In contrast, long-range amplification and PacBio HiFi sequencing fully and directly resolve and phase a wide range of pathogenic variants without inference. To capitalize on the accuracy of HiFi data we designed a new amplicon analysis tool, pbAA. pbAA can rapidly deconvolve a mixture of haplotypes, enabling precise diplotyping, and disease allele classification.
September 6, 2021 |
Revealing Mechanisms of Bacterial Virulence and Adaptation with PacBio SMRT Sequencing
In this talk, speakers will describe the importance of high accuracy and long read length for generating closed bacterial assemblies. Speakers will also share examples of how hard-to-assemble domains and…
August 23, 2021 |
Identifying Key Players in Host-Microbiome Interactions with High Resolution 16S Sequencing
In this talk, speakers provide an understanding of how highly accurate long-read sequencing of extended 16S amplicons enables the identification of metagenome community members at higher taxonomic resolution than short-read…
August 19, 2021 |
Certified Service Provider Profile: In Seoul, DNA Link offers excellence in SMRT Sequencing
Korean service provider DNA Link has established strong expertise with the PacBio sequencing platform in response to high global demand for the technology.
August 19, 2021 |
Technical note — Preparing DNA for PacBio HiFi sequencing – Extraction and quality control
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.
August 19, 2021 | Products, procedures + protocols
Product brochure — Sequel IIe System – Sequencing evolved
Learn how highly accurate long-read sequencing from the Sequel IIe Systems delivers data you can trust for advanced biological insights across a range of applications.
August 19, 2021 | Products, procedures + protocols
Brochure — SMRT Link: Explore and analyze your data with confidence
With SMRT Link you can unlock the power of PacBio Single Molecule, Real-Time (SMRT) Sequencing using our portfolio of software tools designed to set up and monitor sequencing runs, review performance metrics, analyze, visualize, and annotate your sequencing data.
August 19, 2021 | Sample + library preparation
Product note — SMRTbell express template prep 2.0 for microbial multiplexing
The SMRTbell Express Template Prep Kit 2.0 provides a streamlined, single-tube reaction strategy to generate SMRTbell libraries from 500 bp to >50 kb insert size targets to support large-insert genomic libraries, multiplexed microbial genomes and amplicon sequencing. With this new formulation, we have increased both the yield and efficiency of SMRTbell library preparation for SMRT Sequencing while further minimizing handling-induced DNA damage to retain the integrity of genomic DNA (gDNA). This product note highlights the key benefits, performance, and resources available for obtaining complete microbial genome assemblies with multiplexed sequencing. By using a single-tube, addition-only strategy, the streamlined workflow reduces the number of AMPure clean-up steps. This provides an opportunity to explore automation solutions for high-volume projects, while using as little as 1 ug of input DNA.
August 19, 2021 | Products, procedures + protocols
Application note — Microbial multiplexing workflow on the Sequel system
Obtaining microbial genomes with the highest accuracy and contiguity is extremely important when exploring the functional impact of genetic and epigenetic variants on a genome-wide scale. A comprehensive view of the bacterial genome, including genes, regulatory regions, IS elements, phage integration sites, and base modifications is vital to understanding key traits such as antibiotic resistance, virulence, and metabolism. SMRT Sequencing provides complete genomes, often assembled into a single contig. Our streamlined microbial multiplexing procedure for the Sequel System, from library preparation to genome assembly, can be completed with less than 8 hours bench time. Starting with high-quality genomic DNA (gDNA), samples are sheared to approximately 12 kb distribution, ligated with barcoded overhang adapters, pooled at equimolar representation, and sequenced. Demultiplexing of samples is automated, allowing for immediate genome assembly on our SMRT Link analysis software solution.
August 19, 2021 |
PacBio Certified Service Providers
Explore a list of PacBio certified service providers.
August 19, 2021 |
Informational guide — Looking beyond the single reference genome to a pangenome for every species
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.
August 19, 2021 |
Informational guide — Understanding accuracy in DNA sequencing
Learn why it is critically important to understand accuracy in DNA sequencing to distinguish important biological information from sequencing errors.
August 19, 2021 | Infectious disease research
Infographic — A brief history of microbiology
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 microscopic world.