The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
plasmidSPAdes: assembling plasmids from whole genome sequencing data
Open accessAbstract
Motivation: Plasmids are stably maintained extra-chromosomal genetic elements that replicate independently from the host cell’s chromosomes. Although plasmids harbor biomedically important genes, (such as genes involved in virulence and antibiotics resistance), there is a shortage of specialized software tools for extracting and assembling plasmid data from whole genome sequencing projects. Results: We present the plasmidSPAdes algorithm and software tool for assembling plasmids from whole genome sequencing data and benchmark its performance on a diverse set of bacterial genomes. Availability and Implementation: plasmidSPAdes is publicly available at http://spades.bioinf.spbau.ru/plasmidSPAdes/ Contact: d.antipov@spbu.ru Supplementary information: Supplementary data are available at Bioinformatics online.
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QUAST: quality assessment tool for genome assemblies
Gurevich, A., Saveliev, V., Vyahhi, N., & Tesler, G. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt086 · Cited by 11,172
A fast, lock-free approach for efficient parallel counting of occurrences of k -mers
Marçais, G., & Kingsford, C. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr011 · Cited by 4,661
Cited by
Using SPAdes De Novo Assembler
Prjibelski, A., Antipov, D., Meleshko, D., Lapidus, A., & Korobeynikov, A. (2020) · Current Protocols in Bioinformatics · doi:10.1002/cpbi.102 · Cited by 3,555
Self-citationMobile Genetic Elements Associated with Antimicrobial Resistance
Partridge, S. R., Kwong, S. M., Firth, N., & Jensen, S. O. (2018) · Clinical Microbiology Reviews · doi:10.1128/cmr.00088-17 · Cited by 2,751
Antibiotic resistance in microbes: History, mechanisms, therapeutic strategies and future prospects
Uddin, T. M., Chakraborty, A. J., Khusro, A., Zidan, B. R. M., Mitra, S., Emran, T. B., Dhama, K., Ripon, M. K. H., Gajdács, M., Sahibzada, M. U. K., et al. (2021) · Journal of Infection and Public Health · doi:10.1016/j.jiph.2021.10.020 · Cited by 1,311
Sequencing-based methods and resources to study antimicrobial resistance
Boolchandani, M., D’Souza, A. W., & Dantas, G. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0108-4 · Cited by 522
Novel plasmid-mediated colistin resistance gene mcr-7.1 in Klebsiella pneumoniae
Yang, Y.-Q., Li, Y.-X., Lei, C.-W., Zhang, A.-Y., & Wang, H.-N. (2018) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dky111 · Cited by 367
Metadata
- Authors
- Antipov, D., Hartwick, N., Shen, M., Raiko, M., Lapidus, A., & Pevzner, P. A.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2016-07-27
- Volume
- 32
- Issue
- 22
- Pages
- 3380-3387
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2951563276
- Cited by
- 534
- References
- 2
- FWCI
- 23.62
- Type
- journal article
- Language
- en
- Open access
- bronze
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