Nature Communications (Apr 2021)
Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C
- Zev N. Kronenberg,
- Arang Rhie,
- Sergey Koren,
- Gregory T. Concepcion,
- Paul Peluso,
- Katherine M. Munson,
- David Porubsky,
- Kristen Kuhn,
- Kathryn A. Mueller,
- Wai Yee Low,
- Stefan Hiendleder,
- Olivier Fedrigo,
- Ivan Liachko,
- Richard J. Hall,
- Adam M. Phillippy,
- Evan E. Eichler,
- John L. Williams,
- Timothy P. L. Smith,
- Erich D. Jarvis,
- Shawn T. Sullivan,
- Sarah B. Kingan
Affiliations
- Zev N. Kronenberg
- Phase Genomics
- Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute
- Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute
- Gregory T. Concepcion
- Pacific Biosciences
- Paul Peluso
- Pacific Biosciences
- Katherine M. Munson
- Department of Genome Sciences, University of Washington School of Medicine
- David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine
- Kristen Kuhn
- US Meat Animal Research Center, ARS USDA, Clay Center
- Kathryn A. Mueller
- Phase Genomics
- Wai Yee Low
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide
- Stefan Hiendleder
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide
- Olivier Fedrigo
- Vertebrate Genomes Laboratory, The Rockefeller University
- Ivan Liachko
- Phase Genomics
- Richard J. Hall
- Pacific Biosciences
- Adam M. Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute
- Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine
- John L. Williams
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide
- Timothy P. L. Smith
- US Meat Animal Research Center, ARS USDA, Clay Center
- Erich D. Jarvis
- Laboratory of Neurogenetics of Language, The Rockefeller University
- Shawn T. Sullivan
- Phase Genomics
- Sarah B. Kingan
- Pacific Biosciences
- DOI
- https://doi.org/10.1038/s41467-020-20536-y
- Journal volume & issue
-
Vol. 12,
no. 1
pp. 1 – 10
Abstract
Methods to produce haplotype-resolved genome assemblies often rely on access to family trios. The authors present FALCON-Phase, a tool that combines ultra-long range Hi-C chromatin interaction data with a long read de novo assembly to extend haplotype phasing to the contig or scaffold level.
