variant phasing

PgmNr 1866/W: Detection and phasing of small variants in Genome in a Bottle samples with highly accurate long reads

Introduction: Long-read PacBio SMRT Sequencing has been applied successfully to assemble genomes and detect structural variants. However, due to high raw read error rates of 10-15%, it has remained difficult to call small variants from long reads. …

Comprehensive variant detection in a human genome with highly accurate long reads

Introduction: Long-read sequencing has been applied successfully to assemble genomes and detect structural variants. However, due to high raw-read error rates (10-15%), it has remained difficult to call small variants from long reads. Recent …

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

The DNA sequencing technologies in use today produce either highly accurate short reads or less-accurate long reads. We report the optimization of circular consensus sequencing (CCS) to improve the accuracy of single-molecule real-time (SMRT) …

Comprehensive variant detection in a human genome with highly accurate long reads

Introduction: Long-read sequencing has been applied successfully to assemble genomes and detect structural variants. However, due to high raw-read error rates (10-15%), it has remained difficult to call small variants from long reads. Recent …

Advantages of HiFi reads for variant discovery and genome assembly

The PacBio Sequel II System is capable of generating highly accurate, long reads (HiFi reads) that can be used for variant detection and assembly. In this presentation, we demonstrate the utility and provide example workflows for variant detection, …

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 …

Comprehensive Variant Detection with Highly Accurate Long Reads

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 …

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 …