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Assembly of complete diploid phased chromosomes from draft genome sequences

View ORCID ProfileAndrea Minio, View ORCID ProfileNoé Cochetel, View ORCID ProfileAmanda Vondras, View ORCID ProfileMélanie Massonnet, View ORCID ProfileDario Cantu
doi: https://doi.org/10.1101/2021.11.11.468134
Andrea Minio
1Department of Viticulture and Enology, University of California Davis, Davis, CA 95616
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Noé Cochetel
1Department of Viticulture and Enology, University of California Davis, Davis, CA 95616
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Amanda Vondras
1Department of Viticulture and Enology, University of California Davis, Davis, CA 95616
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Mélanie Massonnet
1Department of Viticulture and Enology, University of California Davis, Davis, CA 95616
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  • ORCID record for Mélanie Massonnet
Dario Cantu
1Department of Viticulture and Enology, University of California Davis, Davis, CA 95616
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  • For correspondence: dacantu@ucdavis.edu
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Abstract

De novo genome assembly is essential for genomic research. High-quality genomes assembled into phased pseudomolecules are challenging to produce and often contain assembly errors because of repeats, heterozygosity, or the chosen assembly strategy. Although algorithms that produce partially phased assemblies exist, haploid draft assemblies that may lack biological information remain favored because they are easier to generate and use. We developed HaploSync, a suite of tools that produces fully phased, chromosome-scale diploid genome assemblies, and performs extensive quality control to limit assembly artifacts. HaploSync scaffolds sequences from a draft diploid assembly into phased pseudomolecules guided by a genetic map and/or the genome of a closely related species. HaploSync generates a report that visualizes the relationships between current and legacy sequences, for both haplotypes, and displays their gene and marker content. This quality control helps the user identify misassemblies and guides Haplosync’s correction of scaffolding errors. Finally, HaploSync fills assembly gaps with unplaced sequences and resolves collapsed homozygous regions. In a series of plant, fungal, and animal kingdom case studies, we demonstrate that HaploSync efficiently increases the assembly contiguity of phased chromosomes, improves completeness by filling gaps, corrects scaffolding, and correctly phases highly heterozygous, complex regions.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/andreaminio/haplosync

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted May 02, 2022.
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Assembly of complete diploid phased chromosomes from draft genome sequences
Andrea Minio, Noé Cochetel, Amanda Vondras, Mélanie Massonnet, Dario Cantu
bioRxiv 2021.11.11.468134; doi: https://doi.org/10.1101/2021.11.11.468134
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Assembly of complete diploid phased chromosomes from draft genome sequences
Andrea Minio, Noé Cochetel, Amanda Vondras, Mélanie Massonnet, Dario Cantu
bioRxiv 2021.11.11.468134; doi: https://doi.org/10.1101/2021.11.11.468134

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