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PacBio Literature

  |  2022

Solutions Guide – Public Health Brochure

Detect, track, and characterize pathogens to a new standard of completeness and precision. PacBio® solutions offer unmatched accuracy and long read lengths to support a wide range of pathogen surveillance applications.
  |  2022

Alternative Size Selection Methods for SMRTbell Prep Kit 3.0

PacBio recommends to use size-selection beads are to remove short DNA fragments and enrich for the long fragments that are most valuable for downstream analysis. Although size-selection beads have many advantages, alternative methods — like gels and DNA precipitation — offer more flexibility in defining a size cutoff. This technical note provides guidance for alternative methods of size selection of WGS libraries prepared with the SMRTbell prep kit 3.0.

Application Brief – Measuring DNA methylation with 5-base HiFi sequencing

HiFi sequencing produces long, accurate reads of the 4 DNA bases — A, C, G, and T — that deliver the most comprehensive characterization of genomes. But HiFi sequencing is not limited to characterizing the genome. It simultaneously measures the epigenome by detecting a fifth base — 5mC at CpG sites — without requiring special library preparation like bisulfite treatment. This detects distinct regional epigenetic patterns, accesses methylation in the full genome, and identifies allele-specific methylation.
  |  2022

Technical note – Covaris-g TUBE gDNA shearing for SMRTbell prep kit 3.0

PacBio recommends that DNA shearing for whole genome sequencing be performed on the Diagenode Megaruptor 3 system, which is the only system validated by PacBio for shearing, in order to produce consistent HiFi yield and quality. When a Megaruptor 3 system is unavailable, the Covaris g-TUBE presents an alternative shearing method that does not require instrumentation beyond a standard microcentrifuge. This Technical note provides guidelines for using the Covaris g-TUBE for DNA shearing.
  |  2022

Technical note – Human whole blood sample prep

Sample preparation is a critical factor for whole genome sequencing (WGS) projects that impacts sequencing yield, read length, and ultimately performance for variant calling and genome assembly. Best practices to optimize performance for PacBio HiFi sequencing are to collect whole human blood, store with potassium EDTA as the anticoagulant for fewer than 2 days at 4°C, and extract DNA from 200 μL of blood using the Nanobind CBB Big DNA kit. When it is not possible to extract from fresh samples, storing samples at 4°C maximizes extraction yield and minimizes degradation for at least 9 days.

Application Brief: Uncover Cancer-Specific RNA Isoforms Using Long Read Sequencing

The Iso-Seq method utilizes long-read transcript sequencing to reliably capture full-length transcript isoforms without the need for computational assembly. PacBio’s long-read RNA sequencing is also significantly less error-prone than other long-read sequencing technologies, offering more robust and accurate isoform discovery power.9,10 Future research will continue to explore the complex and mostly unexplored landscape of isoforms across cancer types

Application Brief: Variant detection using whole genome sequencing with HiFi reads – Best Practices

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.
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