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

Abstract

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.