Platanus-allee is a de novo haplotype assembler enabling a comprehensive access to divergent heterozygous regions

Rei Kajitani, Dai Yoshimura, Miki Okuno, Yohei Minakuchi, Hiroshi Kagoshima, Asao Fujiyama, Kaoru Kubokawa, Yuji Kohara, Atsushi Toyoda and Takehiko Itoh ()
Additional contact information
Rei Kajitani: Tokyo Institute of Technology
Dai Yoshimura: Tokyo Institute of Technology
Miki Okuno: Tokyo Institute of Technology
Yohei Minakuchi: Comparative Genomics Laboratory, National Institute of Genetics
Hiroshi Kagoshima: Advanced Genomics Center, National Institute of Genetics
Asao Fujiyama: Advanced Genomics Center, National Institute of Genetics
Kaoru Kubokawa: The University of Tokyo
Yuji Kohara: Advanced Genomics Center, National Institute of Genetics
Atsushi Toyoda: Comparative Genomics Laboratory, National Institute of Genetics
Takehiko Itoh: Tokyo Institute of Technology

Nature Communications, 2019, vol. 10, issue 1, 1-15

Abstract: Abstract The ultimate goal for diploid genome determination is to completely decode homologous chromosomes independently, and several phasing programs from consensus sequences have been developed. These methods work well for lowly heterozygous genomes, but the manifold species have high heterozygosity. Additionally, there are highly divergent regions (HDRs), where the haplotype sequences differ considerably. Because HDRs are likely to direct various interesting biological phenomena, many genomic analysis targets fall within these regions. However, they cannot be accessed by existing phasing methods, and we have to adopt costly traditional methods. Here, we develop a de novo haplotype assembler, Platanus-allee ( http://platanus.bio.titech.ac.jp/platanus2 ), which initially constructs each haplotype sequence and then untangles the assembly graphs utilizing sequence links and synteny information. A comprehensive benchmark analysis reveals that Platanus-allee exhibits high recall and precision, particularly for HDRs. Using this approach, previously unknown HDRs are detected in the human genome, which may uncover novel aspects of genome variability.

Date: 2019
References: Add references at CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-019-09575-2 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-09575-2

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-019-09575-2

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().