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Computational methods for chromosome-scale haplotype reconstruction

Authors
  • Garg, Shilpa1
  • 1 University of Copenhagen, Copenhagen, Denmark , Copenhagen (Denmark)
Type
Published Article
Publication Date
Apr 12, 2021
Volume
22
Issue
1
Identifiers
DOI: 10.1186/s13059-021-02328-9
Source
Springer Nature
License
Green

Abstract

High-quality chromosome-scale haplotype sequences of diploid genomes, polyploid genomes, and metagenomes provide important insights into genetic variation associated with disease and biodiversity. However, whole-genome short read sequencing does not yield haplotype information spanning whole chromosomes directly. Computational assembly of shorter haplotype fragments is required for haplotype reconstruction, which can be challenging owing to limited fragment lengths and high haplotype and repeat variability across genomes. Recent advancements in long-read and chromosome-scale sequencing technologies, alongside computational innovations, are improving the reconstruction of haplotypes at the level of whole chromosomes. Here, we review recent and discuss methodological progress and perspectives in these areas.

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