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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
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.
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.
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