Pendleton, M., Sebra, R., Pang, A. W., Ummat, A., Franzen, O., Rausch, T., Stutz, A. M., Stedman, W., Anantharaman, T., Hastie, A., Dai, H., Fritz, M. H., 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. (August 2015) Assembly and diploid architecture of an individual human genome via single-molecule technologies. Nat Methods, 12 (8). pp. 780-786. ISSN 1548-7105 (Electronic)1548-7091 (Linking)
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Abstract
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.
| Item Type: | Paper |
|---|---|
| Subjects: | bioinformatics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes Investigative techniques and equipment > assays > next generation sequencing |
| CSHL Authors: | |
| Communities: | CSHL Cancer Center Program > Cancer Genetics CSHL labs > McCombie lab CSHL Cancer Center Shared Resources > DNA Sequencing Service |
| Depositing User: | Matt Covey |
| Date: | 12 August 2015 |
| Date Deposited: | 01 Jul 2015 18:51 |
| Last Modified: | 15 Jul 2021 20:48 |
| PMCID: | PMC4646949 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/31605 |
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