August 19, 2021
Infographic — A genome fit for a giant – sequencing the California redwood
Explore how highly accurate long-read sequencing enabled sequencing the large and highly complex California redwood genome.
Asset Tag: Whole Genome Sequencing,
August 19, 2021 | Cancer research
Case Study — Scientists deconstruct cancer complexity through genome and transcriptome analysis
At Cold Spring Harbor Laboratory, scientists used SMRT Sequencing to decode one of the most challenging cancer genomes ever encountered. Along the way, they built a portfolio of open-access analysis tools that will help researchers everywhere make structural variation discoveries with long-read sequencing data.
August 19, 2021
Case Study — Pioneering a pan-genome reference collection
At DuPont Pioneer, DNA sequencing is paramount for R&D to reveal the genetic basis for traits of interest in commercial crops such as maize, soybean, sorghum, sunflower, alfalfa, canola, wheat, rice, and others. They cannot afford to wait the years it has historically taken for high-quality reference genomes to be produced. Nor can they rely on a single reference to represent the genetic diversity in its germplasm.
August 19, 2021 | Microbial sequencing methods
Case Study — Sequencing an historic bacterial collection for the future
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.
August 19, 2021
Case Study — Diving Deep – Revealing the mysteries of marine life with SMRT Sequencing
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.
August 19, 2021 | Products, procedures + protocols
Application brochure — HiFi reads for highly accurate long-read sequencing
Discover the benefits of HiFi reads and learn how highly accurate long-read sequencing provides a single technology solution across a range of applications.
August 19, 2021 | Sequencing methods
Application brief — Whole genome sequencing for de novo assembly
PacBio HiFi reads provide both long read lengths (up to 25 kb) and high accuracy (>99.9%) to quickly and affordably generate contiguous, complete, and correct de novo genome assemblies of even the most complex genomes.
August 19, 2021 | Human genetics research
Application brochure — Scalable human whole genome HiFi sequencing for rare and inherited disease research
PacBio highly accurate long reads – HiFi reads – offer a single-platform solution for rare and inherited disease research, elucidating suspected genetic causes of disease in up to ~50% of cases that have not previously been explained using short-read exome or whole genome sequencing. PacBio offers an efficient workflow, developed in collaboration with Children’s Mercy Kansas City, which provides a scalable solution for sequencing 100s to 1000s of whole human genomes per year on the Sequel II and Sequel IIe Systems.
August 19, 2021 | Infectious disease research
Application brief — Variant detection using whole genome sequencing with HiFi reads
With highly accurate long reads (HiFi reads) from the Sequel II or IIe Systems you can comprehensively detect variants in 100s to 1000s of genomes in a year. HiFi reads provide high precision and recall for single nucleotide variants (SNVs), indels, structural variants (SVs), and copy number variants (CNVs), including in difficult-to-map repetitive regions.
August 19, 2021 | Rare disease
Informational guide — Whole genome sequencing for understanding rare diseases
Learn how PacBio highly accurate long reads enable an improved approach to whole genome sequencing to understand the genetic origins of rare diseases.
August 19, 2021 | Human genetics research
Publication at a Glance — The complete sequence of a human genome
This landmark study by members of the Telomere-to-Telomer Consortium is the first fully complete assembly to be produced 20 years after the initial drafts of the human genome.
June 15, 2021
Uncovering Neurological Disorders Through an Examination of VNTRs
Many neurological diseases result from expansion of unstable variable nucleotide tandem repeats (VNTRs) that influence gene transcription of neighboring genes. In this talk, Dr. Henne Holstege presents research that investigated…
June 1, 2021
Comparative genomics of Shiga toxin-producing Escherichia coli O145:H28 strains associated with the 2007 Belgium and 2010 US outbreaks.
Shiga toxin-producing Escherichia coli (STEC) is an emerging pathogen. Recently there has been a global in the number of outbreaks caused by non-O157 STECs, typically involving six serogroups O26, O45, 0103, 0111, and 0145. STEC O145:H28 has been associated with severe human disease including hemolytic-uremic syndrome (HUS), and is demonstrated by the 2007 Belgian ice-cream-associated outbreak and 2010 US lettuce-associated outbreak, with over 10% of patients developing HUS in each. The goal of this work was to do comparative genomics of strains, clinical and environmental, to investigate genome diversity and virulence evolution of this important foodborne pathogen.
June 1, 2021
Genome sequencing of endosymbiotic bacterial Streptomyces sp. from Antartic lichen using Single Molecule Real-time Sequencing (SMRT) technology.
Along with the advent of next-generation sequencing (NGS) techniques, it has become possible to sequence a microbial genome very quickly with high coverage. Recently, PacificBioscience developed single molecule real-time sequencing (SMRT) technology, 3rd generation sequencing platform, which provide much longer (average read length: 1.5Kb) reads without PCR amplification. We did de novo sequencing of Streptomyces sp. using Illumina GAIIx, Roche 454 and PacBio RS system and compared the data. The endosymbiotic bacteria Streptomyces sp. PAMC 26508 was isolated from Antarctic lichen Psoroma sp. that grows attached rocks on Barton Peninsula, King George Island, Antarctica (62, 13’S, 58, 47’W). With 4 SMRT cells, we could get more than 15x coverage of corrected sequence data for de novo assembly. Comparing the performance of other sequencing platforms, PacBio platform could generate data on similar manner with general mid-level GC content organism. In conclusion, PacBio RS system, SMRT technology, shows better performance with high GC content organisms and is expected to be the new tool to improve the de novo sequencing and assembly.
June 1, 2021
Genome sequencing of microbial genomes using Single Molecule Real-time sequencing (SMRT) technology.
In the last year, high-throughput sequencing technologies have progressed from proof-of-concept to production quality. Although each technology is able to produce vast quantities of sequence information, in every case the underlying chemistry limits reads to very short lengths. We present a examining de novo assembly comparison with bacterial genome assembly varying genome size (from 3.1Mb to 7.6Mb) and different G+C contents (from 43% to 71%), respectively. We analyzed Solexa reads, 454 reads and Pacbio RS reads from Streptomyces sp. (Genome size, 7.6 Mb; G+C content, 71%), Psychrobacter sp. (Genome size, 3.5 Mb; G+C content, 43%), Salinibacterium sp. (Genome size, 3.1 Mb; G+C content, 61%) and Frigoribacterium sp. (Genome size, 3.3 Mb; G+C content, 63%). We assembly each bacterial genome using Celera assembler 7.0 with and without PacBio RS reads. We found out that the assemble result with Pacbio RS reads have less contigs and scaffolds, and better N50 values.