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Cited by 732Genomics and Phylogenetic StudiesGenomic variations and chromosomal abnormalitiesChromosomal and Genetic Variations

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

Open access
Putnam, Nicholas H., O'Connell, Brendan L., Stites, Jonathan C., Rice, Brandon J., Blanchette, Marco, Calef, Robert, Troll, Christopher J., Fields, Andrew +5 more·2016·Genome Research
DOI 10.1101/gr.193474.115PMC PMC4772016
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Abstract

Long-range and highly accurate de novo assembly from short-read data is one of the most pressing challenges in genomics. Recently, it has been shown that read pairs generated by proximity ligation of DNA in chromatin of living tissue can address this problem, dramatically increasing the scaffold contiguity of assemblies. Here, we describe a simpler approach (“Chicago”) based on in vitro reconstituted chromatin. We generated two Chicago data sets with human DNA and developed a statistical model and a new software pipeline (“HiRise”) that can identify poor quality joins and produce accurate, long-range sequence scaffolds. We used these to construct a highly accurate de novo assembly and scaffolding of a human genome with scaffold N50 of 20 Mbp. We also demonstrated the utility of Chicago for improving existing assemblies by reassembling and scaffolding the genome of the American alligator. With a single library and one lane of Illumina HiSeq sequencing, we increased the scaffold N50 of the American alligator from 508 kbp to 10 Mbp.

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  • High-throughput, inexpensive proximity sequencing methods emerged as powerful tools to scaffold subchromosomal genomic contigs into chromosome-scale sequences.

    “High-throughput, inexpensive proximity sequencing methods (reviewed in 83) emerged as powerful tools to scaffold subchromosomal genomic contigs into sequences reconstructing whole chromosomes (i.e., chromosome-scale) (54, 55)”

    From Topological Approaches in Animal Comparative Genomics (2026) · cites this paper as [55]

  • Genome sequencing and assembly have become increasingly affordable and computationally tractable thanks to long-read sequencing technologies, DNA proximity ligation sequencing techniques, and genome sequencing consortia.

    “Genome sequencing and assembly have become increasingly affordable and computationally tractable thanks to the development of long-read sequencing technologies like the Pacific Biosciences and Oxford Nanopore platforms (52); the development of DNA proximity ligation sequencing techniques, like Hi-C, for genome scaffolding (53–55); and the efforts of genome sequencing consortia (1, 2, 4, 56)”

    From Topological Approaches in Animal Comparative Genomics (2026) · cites this paper as [55]

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Cited by

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Authors
Putnam, N. H., O'Connell, B. L., Stites, J. C., Rice, B. J., Blanchette, M., Calef, R., Troll, C. J., Fields, A., Hartley, P. D., Sugnet, C. W., Haussler, D., Rokhsar, D. S., & Green, R. E.
Affiliations
  • Dovetail Genomics (United States) (US)
  • Howard Hughes Medical Institute (US)
  • Joint Genome Institute (US)
  • University of California, Santa Cruz (US)
ORCID
Venue
Genome Research
Publisher
Cold Spring Harbor Laboratory
Published
2016-02-04
Volume
26
Issue
3
Pages
342-350
ISSN
  • 1088-9051 (ISSN-L)
  • 1549-5469
DOI
10.1101/gr.193474.115
PMC
PMC4772016
OpenAlex
W1489349053
Cited by
732
References
3
Citations by year
2026: 19 · 2025: 49 · 2024: 88 · 2023: 79 · 2022: 94 · 2021: 88 · 2020: 89 · 2019: 79 · 2018: 59 · 2017: 53 · 2016: 26 · 2015: 7 · 2014: 1
Type
posted content
Language
en
Open access
Licence
other-oa
Locations
  • Genome Research (publishedVersion, other-oa)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • arXiv (Cornell University) (submittedVersion)
  • OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion, other-oa)
  • eScholarship (California Digital Library) (submittedVersion)
  • HighWire Press Open Archive (submittedVersion)
  • arXiv (Cornell University)
Funders
  • Howard Hughes Medical Institute
  • National Human Genome Research Institute (U54HG007990)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
Keywords
de novo genome assembly, scaffold assembly, human genome assembly, proximity ligation, short-read sequencing
MeSH terms
Animals, Cell Line, Chromosomes, Humans, Genetic Linkage, Reproducibility of Results, Genomic Library, Computational Biology, Genomics, High-Throughput Nucleotide Sequencing

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