Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C
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.
| Main Authors: | , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2021-04-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-020-20536-y |
| _version_ | 1818402908684681216 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Zev N. Kronenberg |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-14T08:15:50Z |
| format | Article |
| id | doaj.art-36f8c0b7e92d40fdb0d367dee6cfc462 |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-12-14T08:15:50Z |
| publishDate | 2021-04-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-36f8c0b7e92d40fdb0d367dee6cfc4622022-12-21T23:09:55ZengNature PortfolioNature Communications2041-17232021-04-0112111010.1038/s41467-020-20536-yExtended haplotype-phasing of long-read de novo genome assemblies using Hi-CZev N. Kronenberg0Arang Rhie1Sergey Koren2Gregory T. Concepcion3Paul Peluso4Katherine M. Munson5David Porubsky6Kristen Kuhn7Kathryn A. Mueller8Wai Yee Low9Stefan Hiendleder10Olivier Fedrigo11Ivan Liachko12Richard J. Hall13Adam M. Phillippy14Evan E. Eichler15John L. Williams16Timothy P. L. Smith17Erich D. Jarvis18Shawn T. Sullivan19Sarah B. Kingan20Phase GenomicsGenome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research InstituteGenome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research InstitutePacific BiosciencesPacific BiosciencesDepartment of Genome Sciences, University of Washington School of MedicineDepartment of Genome Sciences, University of Washington School of MedicineUS Meat Animal Research Center, ARS USDA, Clay CenterPhase GenomicsDavies Research Centre, School of Animal and Veterinary Sciences, The University of AdelaideDavies Research Centre, School of Animal and Veterinary Sciences, The University of AdelaideVertebrate Genomes Laboratory, The Rockefeller UniversityPhase GenomicsPacific BiosciencesGenome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research InstituteDepartment of Genome Sciences, University of Washington School of MedicineDavies Research Centre, School of Animal and Veterinary Sciences, The University of AdelaideUS Meat Animal Research Center, ARS USDA, Clay CenterLaboratory of Neurogenetics of Language, The Rockefeller UniversityPhase GenomicsPacific BiosciencesMethods 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.https://doi.org/10.1038/s41467-020-20536-y |
| spellingShingle | 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 Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C Nature Communications |
| title | Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C |
| title_full | Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C |
| title_fullStr | Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C |
| title_full_unstemmed | Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C |
| title_short | Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C |
| title_sort | extended haplotype phasing of long read de novo genome assemblies using hi c |
| url | https://doi.org/10.1038/s41467-020-20536-y |
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