The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Scaling metagenome sequence assembly with probabilistic de Bruijn graphs
Open accessAbstract
Deep sequencing has enabled the investigation of a wide range of environmental microbial ecosystems, but the high memory requirements for de novo assembly of short-read shotgun sequencing data from these complex populations are an increasingly large practical barrier. Here we introduce a memory-efficient graph representation with which we can analyze the k -mer connectivity of metagenomic samples. The graph representation is based on a probabilistic data structure, a Bloom filter, that allows us to efficiently store assembly graphs in as little as 4 bits per k -mer, albeit inexactly. We show that this data structure accurately represents DNA assembly graphs in low memory. We apply this data structure to the problem of partitioning assembly graphs into components as a prelude to assembly, and show that this reduces the overall memory requirements for de novo assembly of metagenomes. On one soil metagenome assembly, this approach achieves a nearly 40-fold decrease in the maximum memory requirements for assembly. This probabilistic graph representation is a significant theoretical advance in storing assembly graphs and also yields immediate leverage on metagenomic assembly.
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Cites
A human gut microbial gene catalogue established by metagenomic sequencing
MetaHIT Consortium, Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., et al. (2010) · Nature · doi:10.1038/nature08821 · Cited by 11,624
Environmental genome shotgun sequencing of the sargasso sea
Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., Wu, D., Paulsen, I., Nelson, K. E., Nelson, W., et al. (2004) · Science · doi:10.1126/science.1093857 · Cited by 4,376
How to apply de Bruijn graphs to genome assembly
Compeau, P. E. C., Pevzner, P. A., & Tesler, G. (2011) · Nature Biotechnology · doi:10.1038/nbt.2023 · Cited by 673
Cited by
Shotgun metagenomics, from sampling to analysis
Quince, C., Walker, A. W., Simpson, J. T., Loman, N. J., & Segata, N. (2017) · Nature Biotechnology · doi:10.1038/nbt.3935 · Cited by 2,202
Strains, functions and dynamics in the expanded Human Microbiome Project
Lloyd-Price, J., Mahurkar, A., Rahnavard, G., Crabtree, J., Orvis, J., Hall, A. B., Brady, A., Creasy, H. H., McCracken, C., Giglio, M. G., et al. (2017) · Nature · doi:10.1038/nature23889 · Cited by 1,267
Nagarajan, N., & Pop, M. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3367 · Cited by 474
Zhou, J., He, Z., Yang, Y., Deng, Y., Tringe, S. G., & Alvarez-Cohen, L. (2015) · mBio · doi:10.1128/mbio.02288-14 · Cited by 474
Structure and function of the healthy pre-adolescent pediatric gut microbiome
Hollister, E. B., Riehle, K., Luna, R. A., Weidler, E. M., Rubio-Gonzales, M., Mistretta, T.-A., Raza, S., Doddapaneni, H. V., Metcalf, G. A., Muzny, D. M., et al. (2015) · Microbiome · doi:10.1186/s40168-015-0101-x · Cited by 406
Metadata
- Authors
- Pell, J., Hintze, A., Canino-Koning, R., Howe, A., Tiedje, J. M., & Brown, C. T.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2012-07-30
- Volume
- 109
- Issue
- 33
- Pages
- 13272-13277
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2163830511
- Cited by
- 247
- References
- 3
- FWCI
- 11.62
- Type
- journal article
- Language
- en
- Open access
- green
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- Pell, J., Hintze, A., Canino-Koning, R., Howe, A., Tiedje, J. M., & Brown, C. T. (2012). Scaling metagenome sequence assembly with probabilistic de Bruijn graphs. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1121464109
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