Preprint Review Version 1 Preserved in Portico This version is not peer-reviewed

Computational Methods for Chromosome-Scale Haplotype Reconstruction

Version 1 : Received: 4 January 2021 / Approved: 6 January 2021 / Online: 6 January 2021 (12:06:39 CET)

How to cite: Garg, S. Computational Methods for Chromosome-Scale Haplotype Reconstruction. Preprints 2021, 2021010116 (doi: 10.20944/preprints202101.0116.v1). Garg, S. Computational Methods for Chromosome-Scale Haplotype Reconstruction. Preprints 2021, 2021010116 (doi: 10.20944/preprints202101.0116.v1).

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 that spans 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 methodological progress in these areas and discuss perspectives that could enable routine high-quality haplotype reconstruction in clinical and evolutionary studies.

Subject Areas

Bioinformatics; Graphs; Medical genetics; sequencing methods

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