PacBio

Reviewing benchmark v3.3.2 PacBio CCS discrepancies in benchmark v4alpha

Comprehensive Variant Detection with Highly Accurate Long Reads

Recent improvements in library preparation and sequencing chemistry have increased the length, accuracy, and throughput of PacBio Circular Consensus Sequencing (CCS) reads, resulting in 10-20kb reads with average read quality well above 99%. Here we …

Abstract 1738: Characterization of structural variants within MACROD2 in the pathogenesis of colorectal cancer

Background: Cancer is caused by somatic DNA alterations, which comprise small nucleotide variants (SNVs), chromosome somatic copy number alterations (SCNAs) and chromosomal breakpoint structural variants (SVs). Previously, we investigated …

Single Molecule High-Fidelity (HiFi) Sequencing with >10 kb Libraries

Recent improvements in sequencing chemistry and instrument performance combine to create a new PacBio data type, Single Molecule High-Fidelity reads (HiFi reads). Increased read length and improvement in library construction enables average read …

The landscape of SNCA transcripts across synucleinopathies: New insights from long reads sequencing analysis

Dysregulation of alpha-synuclein expression has been implicated in the pathogenesis of synucleinopathies, in particular Parkinson’s Disease (PD) and Dementia with Lewy bodies (DLB). Previous studies have shown that the alternatively spliced isoforms …

Detecting and Phasing Small Variants with Highly Accurate Long Reads

We summarize the challenges around small variant detection for highly accurate (=99%) long reads and present workflow solutions using existing tools (GATK) and new tools (DeepVariant with trained CCS model). Presented at PacBio SMRT Informatics …

Highly-accurate long-read sequencing improves variant detection and assembly of a human genome

The major DNA sequencing technologies in use today produce either highly-accurate short reads or noisy long reads. We developed a protocol based on single-molecule, circular consensus sequencing (CCS) to generate highly-accurate (99.8%) long reads …

Comprehensive Variant Detection in a Human Genome with PacBio High-Fidelity Reads

Human genomic variation ranges in size from single nucleotide substitutions to large chromosomal rearrangements. Sequencing technologies tend to be optimized for detecting particular variant types and sizes. Short reads excel at detecting SNVs and …

PacBio HiFi Variant Detection

Calling all variants with highly accurate long reads

Full-length transcript (Iso-Seq) profiling for improved genome annotations (poster #913)

Incomplete annotation of genomes represents a major impediment to understanding biological processes, functional differences between species, and their evolutionary mechanisms. Often, genes that are large, embedded within duplicated genomic regions, …