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  1. ; ; ; ; ; (, Bioinformatics Advances)
    Fiston-Lavier, Anna-Sophie (Ed.)
    Abstract MotivationHaplotagging is a method for linked-read sequencing, which leverages the cost-effectiveness and throughput of short-read sequencing while retaining part of the long-range haplotype information captured by long-read sequencing. Despite its utility and advantages over similar methods, existing linked-read analytical pipelines are incompatible with haplotagging data. ResultsWe describe Harpy, a modular and user-friendly software pipeline for processing all stages of haplotagged linked-read data, from raw sequence data to phased genotypes and structural variant detection. Availability and implementationhttps://github.com/pdimens/harpy. 
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    Free, publicly-accessible full text available December 26, 2025