The DOI matches its Crossref record; 47 of the 47 references it cites were found in a registry or an index.
The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000
Open accessAbstract
Hi-C contact maps are valuable for genome assembly (Lieberman-Aiden, van Berkum et al. 2009; Burton et al. 2013; Dudchenko et al. 2017). Recently, we developed Juicebox, a system for the visual exploration of Hi-C data (Durand, Robinson et al. 2016), and 3D-DNA, an automated pipeline for using Hi-C data to assemble genomes (Dudchenko et al. 2017). Here, we introduce “Assembly Tools,” a new module for Juicebox, which provides a point-and-click interface for using Hi-C heatmaps to identify and correct errors in a genome assembly. Together, 3D-DNA and the Juicebox Assembly Tools greatly reduce the cost of accurately assembling complex eukaryotic genomes. To illustrate, we generated de novo assemblies with chromosome-length scaffolds for three mammals: the wombat, Vombatus ursinus (3.3Gb), the Virginia opossum, Didelphis virginiana (3.3Gb), and the raccoon, Procyon lotor (2.5Gb). The only inputs for each assembly were Illumina reads from a short insert DNA-Seq library (300 million Illumina reads, maximum length 2x150 bases) and an in situ Hi-C library (100 million Illumina reads, maximum read length 2x150 bases), which cost <$1000.
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Cites
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A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
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Self-citationComprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
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Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments
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Self-citationDe novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds
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Self-citationJuicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom
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Schultz, D. T., Haddock, S. H. D., Bredeson, J. V., Green, R. E., Simakov, O., & Rokhsar, D. S. (2023) · Nature · doi:10.1038/s41586-023-05936-6 · Cited by 362
A beginner's guide to low‐coverage whole genome sequencing for population genomics
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Metadata
- Authors
- Dudchenko, O., Shamim, M. S., Batra, S. S., Durand, N. C., Musial, N. T., Mostofa, R., Pham, M., Glenn St Hilaire, B., Yao, W., Stamenova, E., Hoeger, M., Nyquist, S. K., Korchina, V., Pletch, K., Flanagan, J. P., Tomaszewicz, A., McAloose, D., Pérez Estrada, C., Novak, B. J., Omer, A. D., & Aiden, E. L.
- Venue
- bioRxiv (Cold Spring Harbor Laboratory)
- Publisher
- openRxiv
- Published
- 2018-01-28
- OpenAlex
- W2789849365
- Cited by
- 309
- References
- 47
- Type
- posted content
- Language
- en
- Open access
- green
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- Dudchenko, O., Shamim, M. S., Batra, S. S., Durand, N. C., Musial, N. T., Mostofa, R., Pham, M., Glenn St Hilaire, B., Yao, W., Stamenova, E., Hoeger, M., Nyquist, S. K., Korchina, V., Pletch, K., Flanagan, J. P., Tomaszewicz, A., McAloose, D., Pérez Estrada, C., Novak, B. J., . . . Aiden, E. L. (2018). The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000. bioRxiv (Cold Spring Harbor Laboratory). https://doi.org/10.1101/254797
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