The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
Assembly and diploid architecture of an individual human genome via single-molecule technologies
Open accessAbstract
We present the first comprehensive analysis of a diploid human genome that combines single-molecule sequencing with single-molecule genome maps. Our hybrid assembly markedly improves upon the contiguity observed from traditional shotgun sequencing approaches, with scaffold N50 values approaching 30 Mb, and we identified complex structural variants (SVs) missed by other high-throughput approaches. Furthermore, by combining Illumina short-read data with long reads, we phased both single-nucleotide variants and SVs, generating haplotypes with over 99% consistency with previous trio-based studies. Our work shows that it is now possible to integrate single-molecule and high-throughput sequence data to generate de novo assembled genomes that approach reference quality.
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Cites
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
A map of human genome variation from population-scale sequencing.
The 1000 Genomes Project Consortium (2010) · Nature · doi:10.1038/nature09534 · Cited by 7,877
The Diploid Genome Sequence of an Individual Human
Levy, S., Sutton, G., Ng, P. C., Feuk, L., Halpern, A. L., Walenz, B. P., Axelrod, N., Huang, J., Kirkness, E. F., Denisov, G., et al. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050254 · Cited by 1,778
Self-citationMapping copy number variation by population-scale genome sequencing
1000 Genomes Project, Mills, R. E., Walter, K., Stewart, C., Handsaker, R. E., Chen, K., Alkan, C., Abyzov, A., Yoon, S. C., Ye, K., et al. (2011) · Nature · doi:10.1038/nature09708 · Cited by 1,140
The fragment assembly string graph
Myers, E. W. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti1114 · Cited by 424
Cited by
Coming of age: ten years of next-generation sequencing technologies
Goodwin, S., McPherson, J. D., & McCombie, W. R. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.49 · Cited by 4,352
Self-citationMerqury: reference-free quality, completeness, and phasing assessment for genome assemblies
Rhie, A., Walenz, B. P., Koren, S., & Phillippy, A. M. (2020) · Genome Biology · doi:10.1186/s13059-020-02134-9 · Cited by 3,643
An integrated map of structural variation in 2,504 human genomes
Sudmant, P. H., Rausch, T., Gardner, E. J., Handsaker, R. E., Abyzov, A., Huddleston, J., Zhang, Y., Ye, K., Jun, G., Hsi-Yang Fritz, M., et al. (2015) · Nature · doi:10.1038/nature15394 · Cited by 2,354
Self-citationNanopore sequencing and assembly of a human genome with ultra-long reads
Jain, M., Koren, S., Miga, K. H., Quick, J., Rand, A. C., Sasani, T. A., Tyson, J. R., Beggs, A. D., Dilthey, A. T., Fiddes, I. T., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4060 · Cited by 1,892
A chromosome conformation capture ordered sequence of the barley genome
Mascher, M., Gundlach, H., Himmelbach, A., Beier, S., Twardziok, S. O., Wicker, T., Radchuk, V., Dockter, C., Hedley, P. E., Russell, J., et al. (2017) · Nature · doi:10.1038/nature22043 · Cited by 1,450
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Metadata
- Authors
- Pendleton, M., Sebra, R., Pang, A. W. C., Ummat, A., Franzen, O., Rausch, T., Stütz, A. M., Stedman, W., Anantharaman, T., Hastie, A., Dai, H., Fritz, M. H.-Y., Cao, H., Cohain, A., Deikus, G., Durrett, R. E., Blanchard, S. C., Altman, R., Chin, C.-S., Guo, Y., Paxinos, E. E., Korbel, J. O., Darnell, R. B., McCombie, W. R., Kwok, P.-Y., Mason, C. E., Schadt, E. E., & Bashir, A.
- Venue
- Nature Methods
- Published
- 2015-06-29
- Volume
- 12
- Issue
- 8
- Pages
- 780-786
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W1791377616
- Cited by
- 474
- References
- 5
- FWCI
- 27.27
- Type
- journal article
- Language
- en
- Open access
- green
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- Pendleton, M., Sebra, R., Pang, A. W. C., Ummat, A., Franzen, O., Rausch, T., Stütz, A. M., Stedman, W., Anantharaman, T., Hastie, A., Dai, H., Fritz, M. H.-Y., Cao, H., Cohain, A., Deikus, G., Durrett, R. E., Blanchard, S. C., Altman, R., Chin, C.-S., . . . Bashir, A. (2015). Assembly and diploid architecture of an individual human genome via single-molecule technologies. Nature Methods. https://doi.org/10.1038/nmeth.3454
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
