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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.
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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