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.

Tertiary hero overlay

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

Sprite decoration


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.

sample prep beaker icon

Sample preparation

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

hifi sequencing sequel icon


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.

data analysis icon

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

Sprite decoration

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.


Talk with an expert

If you have a question, need to check the status of an order, or are interested in purchasing an instrument, we're here to help.