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. 2023:2590:139-147.
doi: 10.1007/978-1-0716-2819-5_9.

HapCUT2: A Method for Phasing Genomes Using Experimental Sequence Data

Vikas Bansal  1
Affiliations

HapCUT2: A Method for Phasing Genomes Using Experimental Sequence Data

Vikas Bansal. Methods Mol Biol. 2023.

Abstract

Rapid advances in high-throughput DNA sequencing technologies have enabled variant discovery from whole-genome sequencing (WGS) datasets; however linking variants on a chromosome together into haplotypes, also known as haplotype phasing, remains difficult. Human genomes are diploid and haplotype phasing is crucial for the complete interpretation and analysis of genetic variation.Hapcut2 ( https://github.com/vibansal/HapCUT2 ) is an open-source software for phasing diploid genomes using sequence data generated using different sequencing technologies and experimental methods. In this article, we give an overview of the algorithm used by Hapcut2 and describe how to use Hapcut2 for haplotype phasing of individual genomes using different types of sequence data.

Keywords: Haplotype; Haplotype assembly; Long reads; Next-generation sequencing; Phasing; Proximity-ligation; Variants.

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