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SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
Open accessAbstract
The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.
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De 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
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Cited by
QUAST: quality assessment tool for genome assemblies
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Self-citationAssembly of long, error-prone reads using repeat graphs
Kolmogorov, M., Yuan, J., Lin, Y., & Pevzner, P. A. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0072-8 · Cited by 5,986
Self-citationmetaSPAdes: a new versatile metagenomic assembler
Nurk, S., Meleshko, D., Korobeynikov, A., & Pevzner, P. A. (2017) · Genome Research · doi:10.1101/gr.213959.116 · Cited by 4,496
Self-citationMash: fast genome and metagenome distance estimation using MinHash
Ondov, B. D., Treangen, T. J., Melsted, P., Mallonee, A. B., Bergman, N. H., Koren, S., & Phillippy, A. M. (2016) · Genome biology · doi:10.1186/s13059-016-0997-x · Cited by 3,373
ResFinder 4.0 for predictions of phenotypes from genotypes
Bortolaia, V., Kaas, R. S., Ruppe, E., Roberts, M. C., Schwarz, S., Cattoir, V., Philippon, A., Allesoe, R. L., Rebelo, A. R., Florensa, A. F., et al. (2020) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkaa345 · Cited by 3,373
Metadata
- Authors
- Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., Lesin, V. M., Nikolenko, S. I., Pham, S., Prjibelski, A. D., Pyshkin, A. V., Sirotkin, A. V., Vyahhi, N., Tesler, G., Alekseyev, M. A., & Pevzner, P. A.
- Venue
- Journal of Computational Biology
- Publisher
- SAGE Publications
- Published
- 2012-05
- Volume
- 19
- Issue
- 5
- Pages
- 455-477
- ISSN
- 1066-5277 (ISSN-L)
- 1557-8666
- OpenAlex
- W2120902911
- Cited by
- 25,987
- References
- 1
- FWCI
- 77.60
- Type
- journal article
- Language
- en
- Open access
- green
- Licence
- journals.sagepub.com/page/policies/text-and-data-mining-license (tdm)
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- Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., Lesin, V. M., Nikolenko, S. I., Pham, S., Prjibelski, A. D., Pyshkin, A. V., Sirotkin, A. V., Vyahhi, N., Tesler, G., Alekseyev, M. A., & Pevzner, P. A. (2012). SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. Journal of Computational Biology. https://doi.org/10.1089/cmb.2012.0021
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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