March 9, 2023 | Pharmacogenomics
Asset Type: Poster
January 30, 2023 | Agrigenomics
Ultra-high throughput multiomic analysis for agrigenomics on PacBio Revio system
January 30, 2023 | Sample + library preparation
With Nanobind HMW DNA extraction, PacBio provides a complete end-to-end workflow for high-quality genomes from a diversity of samples
January 30, 2023 | Cancer research
MAS-Seq: Towards isoform resolution single-cell transcriptomics using highly accurate long-read sequencing
January 26, 2023 | Metagenomics
Maximizing MAGs from long-read metagenomic assemblies: a new post-assembly pipeline with circular-aware binning
December 15, 2022 | Pharmacogenomics
Accurate CYP2D6 star (*) allele diplotyping for long-read PacBio HiFi sequencing
December 15, 2022 | Human genetics research
High-throughput workflow for human whole genome sequencing using PacBio HiFi
December 15, 2022 | Human genetics research
PacBio HiFi sequencing provides highly accurate CpG methylation calls without bisulfite treatment
November 22, 2022 | Metagenomics
Maximizing MAGs from long-read metagenomic assemblies: a new post-assembly pipeline with circular-aware binning
There are many challenges involved with metagenome assembly, including the presence of multiple species, uneven species abundances, and conserved genomic regions that are shared across species. Highly accurate long reads offer clear advantages over short reads and can overcome many of the obstacles associated with metagenome assembly. PacBio HiFi sequencing of metagenomic samples with the Sequel IIe system regularly produces reads 8–15 kb in size with a median QV ranging from 30 – 45 (99.9–99.99% accuracy). With the development of new metagenome assembly algorithms specific to HiFi reads (hifiasm-meta, metaFlye), it is now possible to reconstruct full metagenome assembled genomes (MAGs) for many high abundance species. These MAGs are often composed of a single circular contig, representing high-quality complete bacterial genomes. However, discontiguous assemblies still occur for lower abundance taxa, and post-assembly tools are required to identify MAGs in this category. Here, we present the HiFi-MAG-Pipeline, a comprehensive workflow for processing long-read metagenome assemblies.
November 3, 2022 | Microbial sequencing methods
Evaluation of taxonomic profiling methods for long-read shotgun metagenomic sequencing datasets
Long-read shotgun metagenomic sequencing is gaining in popularity and offers many advantages over short-read sequencing. The higher information content in long reads is useful for taxonomic profiling, where the main goal is to identify the species present in a microbiome sample (typically bacteria, archaea, fungi, viruses) and their relative abundances. The development of long-read specific tools for taxonomic profiling is accelerating, yet there is a lack of consensus regarding their relative performance. We performed a critical benchmarking study using five long-read methods and four popular short-read methods. We applied these tools to several mock community datasets generated using PacBio HiFi sequencing or Oxford Nanopore Technology (ONT) sequencing, and Illumina data.
November 3, 2022 | Microbial sequencing methods
High MAG recovery and precision species profiling of a pooled human fecal reference using PacBio HiFi sequencing
Advancements in sequencing technologies have made metagenomic analyses of complex microbial samples routine and accessible. Mock communities of known composition are often run in parallel to allow for accurate data evaluation and to facilitate cross-study and inter-lab comparisons, yet they lack the microbial diversity of real-world samples. The ZymoBIOMICS Fecal Reference with TruMatrix Technology (D6323) is a highly diverse pooled human fecal reference that provides a truly complex alternative to mock communities. However, the microbial content of this standard is only partially characterized, and species level composition remains underexplored. Here, we explore the content of this sample using highly accurate long-read sequencing.
October 24, 2022 | Metagenomics
Maximizing MAGs from long-read metagenomic assemblies – a new post-assembly pipeline with circular binning
There are many challenges involved with metagenome assembly, including the presence of multiple species, uneven species abundances, and conserved genomic regions that are shared across species. Highly accurate long reads offer clear advantages over short reads and can overcome many of the obstacles associated with metagenome assembly. PacBio HiFi sequencing of metagenomic samples with the Sequel IIe system regularly produces reads 8–15 kb in size with a median QV ranging from 30–45 (99.9–99.99% accuracy). With the development of new metagenome assembly algorithms specific to HiFi reads (hifiasm-meta, metaFlye), it is now possible to reconstruct full metagenome assembled genomes (MAGs) for many high abundance species. These MAGs are often composed of a single circular contig, representing high-quality complete bacterial genomes. However, discontiguous assemblies still occur for lower abundance taxa, and post-assembly tools are required to identify MAGs in this category. Here, we present the HiFi-MAG-Pipeline, a comprehensive workflow for processing long-read metagenome assemblies.
September 21, 2022 | Metagenomics
Evaluation of taxonomic profiling methods for long-read shotgun metagenomic sequencing datasets
July 12, 2022 |
Integrated heteroduplex correction in PacBio’s circular consensus algorithm
1Pacific Biosciences (PacBio), Menlo Park, United States; 2Baylor College of Medicine, Human Genome Sequencing Center, Houston, United States Background/Objectives: A heteroduplex is a double-stranded sequence comprised of two non-complementary strands…