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Related Experiment Video

Updated: Jul 5, 2025

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

HiPhase: jointly phasing small, structural, and tandem repeat variants from HiFi sequencing.

James M Holt¹, Christopher T Saunders¹, William J Rowell¹

¹Computational Biology, PacBio, 1305 O'Brien Drive, Menlo Park, CA 94025, United States.

Bioinformatics (Oxford, England)

|January 25, 2024

Summary

HiPhase is a new tool that phases small and large variants, including structural and tandem repeats, using long, accurate PacBio HiFi sequencing reads. It improves upon existing methods for variant phasing in diploid organisms.

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Area of Science:

Genomics
Bioinformatics

Background:

Phasing in diploid organisms assigns alleles to haplotypes.
PacBio HiFi reads offer long, accurate data for variant calling and phasing.
Current tools often fail to phase larger variants like structural or tandem repeats.

Purpose of the Study:

To develop a tool that jointly phases various variant types, including small and large variants.
To improve the accuracy and contiguity of haplotype phasing.

Main Methods:

Developed HiPhase, a novel phasing tool.
Utilized dual-mode allele assignment for large variant detection.
Applied the A*-algorithm for efficient phasing.
Incorporated logic to span phase block breaks caused by alignment issues.

Main Results:

HiPhase achieved an average phase block N50 of 480 kb with 929 switchflip errors.
Fully phased 93.8% of genes, outperforming the state of the art.
Jointly phases SNVs, indels, structural, and tandem repeat variants.
Includes multi-threading and concurrent phased alignment output.

Conclusions:

HiPhase effectively phases a comprehensive range of genetic variants using PacBio HiFi reads.
The tool enhances the contiguity and accuracy of haplotype phasing.
HiPhase represents a significant advancement in variant phasing capabilities.