The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
Efficient de novo assembly of large genomes using compressed data structures
Open accessAbstract
De novo genome sequence assembly is important both to generate new sequence assemblies for previously uncharacterized genomes and to identify the genome sequence of individuals in a reference-unbiased way. We present memory efficient data structures and algorithms for assembly using the FM-index derived from the compressed Burrows-Wheeler transform, and a new assembler based on these called SGA (S tring G raph A ssembler). We describe algorithms to error-correct, assemble, and scaffold large sets of sequence data. SGA uses the overlap-based string graph model of assembly, unlike most de novo assemblers that rely on de Bruijn graphs, and is simply parallelizable. We demonstrate the error correction and assembly performance of SGA on 1.2 billion sequence reads from a human genome, which we are able to assemble using 54 GB of memory. The resulting contigs are highly accurate and contiguous, while covering 95% of the reference genome (excluding contigs <200 bp in length). Because of the low memory requirements and parallelization without requiring inter-process communication, SGA provides the first practical assembler to our knowledge for a mammalian-sized genome on a low-end computing cluster.
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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
Self-citationAccurate whole human genome sequencing using reversible terminator chemistry
Bentley, D. R., Balasubramanian, S., Swerdlow, H. P., Smith, G. P., Milton, J., Brown, C. G., Hall, K. P., Evers, D. J., Barnes, C. L., Bignell, H. R., et al. (2008) · Nature · doi:10.1038/nature07517 · Cited by 3,684
Self-citationDe novo assembly of human genomes with massively parallel short read sequencing
Li, R., Zhu, H., Ruan, J., Qian, W., Fang, X., Shi, Z., Li, Y., Li, S., Shan, G., Kristiansen, K., et al. (2010) · Genome Research · doi:10.1101/gr.097261.109 · Cited by 2,926 · cited 7×
“Currently available assemblers require either a single computer with very large amounts of memory—typically in the hundreds of gigabytes (Li et al. 2010b; Gnerre et al. 2011)—or a large distributed cluster of tightly coupled computers (Simpson et al. 2009; Boisvert et al. 2010).”
BackgroundMethodInfluentialThe sequence and de novo assembly of the giant panda genome
Li, R., Fan, W., Tian, G., Zhu, H., He, L., Cai, J., Huang, Q., Cai, Q., Li, B., Bai, Y., et al. (2010) · Nature · doi:10.1038/nature08696 · Cited by 1,180
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Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum
Shen, X.-X., Opulente, D. A., Kominek, J., Zhou, X., Steenwyk, J. L., Buh, K. V., Haase, M. A. B., Wisecaver, J. H., Wang, M., Doering, D. T., et al. (2018) · Cell · doi:10.1016/j.cell.2018.10.023 · Cited by 619
Nagarajan, N., & Pop, M. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3367 · Cited by 474
Sahraeian, S. M. E., Mohiyuddin, M., Sebra, R., Tilgner, H., Afshar, P. T., Au, K. F., Bani Asadi, N., Gerstein, M. B., Wong, W. H., Snyder, M. P., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-00050-4 · Cited by 376
Postglacial viability and colonization in North America’s ice-free corridor
Pedersen, M. W., Ruter, A., Schweger, C., Friebe, H., Staff, R. A., Kjeldsen, K. K., Mendoza, M. L. Z., Beaudoin, A. B., Zutter, C., Larsen, N. K., et al. (2016) · Nature · doi:10.1038/nature19085 · Cited by 369
Ye, C., Hill, C. M., Wu, S., Ruan, J., & Ma, Z. (2016) · Scientific Reports · doi:10.1038/srep31900 · Cited by 304
DNA-Based Storage: Trends and Methods
Yazdi, S. M. H. T., Kiah, H. M., Garcia-Ruiz, E., Ma, J., Zhao, H., & Milenkovic, O. (2015) · IEEE Transactions on Molecular, Biological and Multi-Scale Communications · doi:10.1109/tmbmc.2016.2537305 · Cited by 278
Vollmers, J., Wiegand, S., & Kaster, A.-K. (2017) · PLoS ONE · doi:10.1371/journal.pone.0169662 · Cited by 240
Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts
Steenwyk, J. L., Opulente, D. A., Kominek, J., Shen, X.-X., Zhou, X., Labella, A. L., Bradley, N. P., Eichman, B. F., Čadež, N., Libkind, D., et al. (2019) · PLoS Biology · doi:10.1371/journal.pbio.3000255 · Cited by 162
Reference-assisted chromosome assembly
Kim, J., Larkin, D. M., Cai, Q., Asan, Zhang, Y., Ge, R.-L., Auvil, L., Capitanu, B., Zhang, G., Lewin, H. A., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1220349110 · Cited by 128
Rubino, F., Carberry, C., Waters, S. M., Kenny, D., McCabe, M. S., & Creevey, C. J. (2017) · The ISME Journal · doi:10.1038/ismej.2016.172 · Cited by 101
Tørresen, O. K., Brieuc, M. S. O., Solbakken, M. H., Sørhus, E., Nederbragt, A. J., Jakobsen, K. S., Meier, S., Edvardsen, R. B., & Jentoft, S. (2018) · BMC Genomics · doi:10.1186/s12864-018-4616-y · Cited by 46
Roscito, J. G., Sameith, K., Kirilenko, B. M., Hecker, N., Winkler, S., Dahl, A., Rodrigues, M. T., & Hiller, M. (2022) · Cell Reports · doi:10.1016/j.celrep.2021.110280 · Cited by 44
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Metadata
- Authors
- Simpson, J. T., & Durbin, R.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2011-12-07
- Volume
- 22
- Issue
- 3
- Pages
- 549-556
- ISSN
- 1088-9051 (ISSN-L)
- OpenAlex
- W2115501618
- Cited by
- 768
- References
- 4
- Type
- posted content
- Language
- en
- Open access
- hybrid
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