Variant detection

PacBio highly accurate long reads (HiFi reads) provide comprehensive detection of all variants in a genome. Increased variant detection improves power to link genetics to phenotypes of interests for novel discovery of genes and causative variants.

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Calling all variant types

Variation between two human genomes, by number of base pairs impacted — Single nucleotide variants (SNVs); insertions and deletions (indels) involve fewer than 50 base pairs; structural variants (SVs) consist of greater than 50 base pairs. PacBio highly accurate long reads enable comprehensive detection of all variant types.

Types of variants - PacBio

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Workflow

From DNA to comprehensive variant detection

With HiFi reads from the Sequel II or IIe systems, you can comprehensively detect variants in hundreds to thousands 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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Sample preparation

Starting with unamplified genomic DNA, prepare libraries for whole genome sequencing using standardized protocols and workflow recommendations.

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Sequencing

The Sequel IIe system provides affordable HiFi coverage of a genome for comprehensive variant detection on a single platform.

  • Use the Sequel II or IIe system and SMRT Cell 8M to sequence to desired coverage depth
  • Recommend 2 SMRT Cells 8M to achieve >15-fold coverage of a human genome for comprehensive variant detection*

*Read lengths, reads/data per SMRT Cell 8M, and other sequencing performance results vary based on sample quality/type and insert size.

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Data analysis

Detect variants of all types using efficient, full-solution analytical software tools and standard file formats.

  • Call structural variants with pbsv, available through the structural variant calling analysis in SMRT Link
  • Call small variants with DeepVariant using the PacBio model
  • Use joint calling in pbsv and DeepVariant for multiple samples
  • Phase variants with WhatsHap

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Scalable human whole genome HiFi sequencing for rare and inherited disease research

Explore our efficient and scalable workflow, developed in collaboration with Children’s Mercy Kansas City, for high-throughput sequencing and comprehensive variant detection to better understand the genetic causes of rare and inherited diseases.

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