The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
High-quality draft assemblies of mammalian genomes from massively parallel sequence data
Open accessAbstract
Massively parallel DNA sequencing technologies are revolutionizing genomics by making it possible to generate billions of relatively short (~100-base) sequence reads at very low cost. Whereas such data can be readily used for a wide range of biomedical applications, it has proven difficult to use them to generate high-quality de novo genome assemblies of large, repeat-rich vertebrate genomes. To date, the genome assemblies generated from such data have fallen far short of those obtained with the older (but much more expensive) capillary-based sequencing approach. Here, we report the development of an algorithm for genome assembly, ALLPATHS-LG, and its application to massively parallel DNA sequence data from the human and mouse genomes, generated on the Illumina platform. The resulting draft genome assemblies have good accuracy, short-range contiguity, long-range connectivity, and coverage of the genome. In particular, the base accuracy is high (≥99.95%) and the scaffold sizes (N50 size = 11.5 Mb for human and 7.2 Mb for mouse) approach those obtained with capillary-based sequencing. The combination of improved sequencing technology and improved computational methods should now make it possible to increase dramatically the de novo sequencing of large genomes. The ALLPATHS-LG program is available at http://www.broadinstitute.org/science/programs/genome-biology/crd .
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Cites
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BackgroundMethodInfluentialGenome sequence, comparative analysis and haplotype structure of the domestic dog
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Self-citationThe Diploid Genome Sequence of an Individual Human
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Genome analysis of the platypus reveals unique signatures of evolution
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Cited by
FLASH: fast length adjustment of short reads to improve genome assemblies
Magoč, T., & Salzberg, S. L. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr507 · Cited by 15,366
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Genome structural variation discovery and genotyping
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Repetitive DNA and next-generation sequencing: computational challenges and solutions
Treangen, T. J., & Salzberg, S. L. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3117 · Cited by 1,597
Initial impact of the sequencing of the human genome
Lander, E. S. (2011) · Nature · doi:10.1038/nature09792 · Cited by 1,044
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Metadata
- Authors
- Gnerre, S., MacCallum, I., Przybylski, D., Ribeiro, F. J., Burton, J. N., Walker, B. J., Sharpe, T., Hall, G., Shea, T. P., Sykes, S., Berlin, A. M., Aird, D., Costello, M., Daza, R., Williams, L., Nicol, R., Gnirke, A., Nusbaum, C., Lander, E. S., & Jaffe, D. B.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2010-12-27
- Volume
- 108
- Issue
- 4
- Pages
- 1513-1518
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2022986961
- Cited by
- 1,533
- References
- 9
- FWCI
- 27.53
- Type
- journal article
- Language
- en
- Open access
- green
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