The DOI matches its Crossref record; 26 of the 26 references it cites were found in a registry or an index.
Solving the Problem of Comparing Whole Bacterial Genomes across Different Sequencing Platforms
Open accessAbstract
Whole genome sequencing (WGS) shows great potential for real-time monitoring and identification of infectious disease outbreaks. However, rapid and reliable comparison of data generated in multiple laboratories and using multiple technologies is essential. So far studies have focused on using one technology because each technology has a systematic bias making integration of data generated from different platforms difficult. We developed two different procedures for identifying variable sites and inferring phylogenies in WGS data across multiple platforms. The methods were evaluated on three bacterial data sets and sequenced on three different platforms (Illumina, 454, Ion Torrent). We show that the methods are able to overcome the systematic biases caused by the sequencers and infer the expected phylogenies. It is concluded that the cause of the success of these new procedures is due to a validation of all informative sites that are included in the analysis. The procedures are available as web tools.
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Cites
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Fast and accurate short read alignment with Burrows-Wheeler transform
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BEDTools: a flexible suite of utilities for comparing genomic features
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FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
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Self-citationWalker, T. M., Ip, C. L., Harrell, R. H., Evans, J. T., Kapatai, G., Dedicoat, M. J., Eyre, D. W., Wilson, D. J., Hawkey, P. M., Crook, D. W., et al. (2013) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(12)70277-3 · Cited by 918
Staphylococcus aureus CC398: Host Adaptation and Emergence of Methicillin Resistance in Livestock
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Self-citationTransforming clinical microbiology with bacterial genome sequencing
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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
Self-citationFlorensa, A. F., Kaas, R. S., Clausen, P. T. L. C., Aytan-Aktug, D., & Aarestrup, F. M. (2022) · Microbial Genomics · doi:10.1099/mgen.0.000748 · Cited by 695
Self-citationWhole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis
Quainoo, S., Coolen, J. P. M., van Hijum, S. A. F. T., Huynen, M. A., Melchers, W. J. G., van Schaik, W., & Wertheim, H. F. L. (2017) · Clinical Microbiology Reviews · doi:10.1128/cmr.00016-17 · Cited by 458
Host genetic regulation of human gut microbial structural variation
Zhernakova, D. V., Wang, D., Liu, L., Andreu-Sánchez, S., Zhang, Y., Ruiz-Moreno, A. J., Peng, H., Plomp, N., Del Castillo-Izquierdo, Á., Gacesa, R., et al. (2024) · Nature · doi:10.1038/s41586-023-06893-w · Cited by 174
Campylobacter jejuni transcriptional and genetic adaptation during human infection
Crofts, A. A., Poly, F. M., Ewing, C. P., Kuroiwa, J. M., Rimmer, J. E., Harro, C., Sack, D., Talaat, K. R., Porter, C. K., Gutierrez, R. L., et al. (2018) · Nature Microbiology · doi:10.1038/s41564-018-0133-7 · Cited by 85
Metadata
- Authors
- Kaas, R. S., Leekitcharoenphon, P., Aarestrup, F. M., & Lund, O.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2014-08-11
- Volume
- 9
- Issue
- 8
- Pages
- e104984
- ISSN
- 1932-6203 (ISSN-L)
- OpenAlex
- W2032519858
- Cited by
- 931
- References
- 26
- FWCI
- 9.61
- Type
- journal article
- Language
- en
- Open access
- gold
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