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Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3

Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3

Published on: December 27, 2010

Harpy: a pipeline for processing haplotagging linked-read data.

Pavel V Dimens¹, Ryan P Franckowiak¹, Azwad Iqbal¹

¹Department of Natural Resources and the Environment, Cornell University, Ithaca, NY 14853, United States.

Bioinformatics Advances

|June 27, 2025

Summary

This summary is machine-generated.

Harpy is a new software pipeline designed for haplotagging, a linked-read sequencing method. It processes haplotagged data to enable phased genotypes and structural variant detection, overcoming limitations of existing pipelines.

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Area of Science:

Genomics and Bioinformatics
Molecular Biology

Background:

Haplotagging combines short-read sequencing cost-effectiveness with long-read haplotype information.
Existing analytical pipelines are not compatible with haplotagging data, limiting its application.

Purpose of the Study:

To introduce Harpy, a novel software pipeline for processing haplotagged linked-read data.
To provide a user-friendly and modular solution for the entire analysis workflow.

Main Methods:

Development of a modular software pipeline named Harpy.
Implementation of algorithms for processing raw sequence data from haplotagging.
Integration of tools for phased genotype and structural variant detection.

Main Results:

Harpy successfully processes all stages of haplotagged linked-read data.
The pipeline is modular and user-friendly, facilitating adoption.
Enables accurate phased genotype and structural variant detection from haplotagged data.

Conclusions:

Harpy addresses the incompatibility of existing pipelines with haplotagging data.
This software enhances the utility of haplotagging for genomic analysis.
Harpy provides a comprehensive solution for haplotagged data processing and variant discovery.