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De novo assembly of haplotype-resolved genomes with trio binning.
Koren, Sergey; Rhie, Arang; Walenz, Brian P; Dilthey, Alexander T; Bickhart, Derek M; Kingan, Sarah B; Hiendleder, Stefan; Williams, John L; Smith, Timothy P L; Phillippy, Adam M.
Afiliación
  • Koren S; Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA.
  • Rhie A; Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA.
  • Walenz BP; Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA.
  • Dilthey AT; Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA.
  • Bickhart DM; Institute of Medical Microbiology, Heinrich-Heine-University Düsseldorf, Düsseldorf, North Rhine-Westphalia, Germany.
  • Kingan SB; Cell Wall Biology and Utilization Laboratory, ARS USDA, Madison, Wisconsin, USA.
  • Hiendleder S; Pacific Biosciences, Menlo Park, California, USA.
  • Williams JL; Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy SA, Australia.
  • Smith TPL; Robinson Research Institute, The University of Adelaide, Adelaide SA, Australia.
  • Phillippy AM; Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy SA, Australia.
Nat Biotechnol ; 2018 Oct 22.
Article en En | MEDLINE | ID: mdl-30346939
Complex allelic variation hampers the assembly of haplotype-resolved sequences from diploid genomes. We developed trio binning, an approach that simplifies haplotype assembly by resolving allelic variation before assembly. In contrast with prior approaches, the effectiveness of our method improved with increasing heterozygosity. Trio binning uses short reads from two parental genomes to first partition long reads from an offspring into haplotype-specific sets. Each haplotype is then assembled independently, resulting in a complete diploid reconstruction. We used trio binning to recover both haplotypes of a diploid human genome and identified complex structural variants missed by alternative approaches. We sequenced an F1 cross between the cattle subspecies Bos taurus taurus and Bos taurus indicus and completely assembled both parental haplotypes with NG50 haplotig sizes of >20 Mb and 99.998% accuracy, surpassing the quality of current cattle reference genomes. We suggest that trio binning improves diploid genome assembly and will facilitate new studies of haplotype variation and inheritance.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: Nat Biotechnol Asunto de la revista: BIOTECNOLOGIA Año: 2018 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Estados Unidos
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: Nat Biotechnol Asunto de la revista: BIOTECNOLOGIA Año: 2018 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Estados Unidos