Pavel V Dimens, Ryan P Franckowiak, Azwad Iqbal, Jennifer K Grenier, Paul R Munn, Nina Overgaard Therkildsen
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Harpy: a pipeline for processing haplotagging linked-read data.
Motivation: Haplotagging 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.
Results: We 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 implementation: https://github.com/pdimens/harpy.
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