| Autor: |
Sergio Arredondo-Alonso, Rebecca A. Gladstone, Anna K. Pöntinen, João A. Gama, Anita C. Schürch, Val F. Lanza, Pål Jarle Johnsen, Ørjan Samuelsen, Gerry Tonkin-Hill, Jukka Corander |
| Rok vydání: |
2022 |
| Popis: |
Extrachromosomal elements of bacterial cells such as plasmids are notorious for their importance in evolution and adaptation to changing ecology. However, high-resolution population-wide analysis of plasmids has only become accessible recently with the advent of scalable long-read sequencing technology. Current typing methods for the classification of plasmids remain limited in their scope which motivated us to develop a computationally efficient approach to simultaneously recognize novel types and classify plasmids into previously identified groups. Our method can easily handle thousands of input sequences which are compressed using a unitig representation in a de Bruijn graph. We provide an intuitive visualization, classification and clustering scheme that users can explore interactively. This provides a framework that can be easily distributed and replicated, enabling a consistent labelling of plasmids across past, present, and future sequence collections. We illustrate the attractive features of our approach by the analysis of population-wide plasmid data from the opportunistic pathogenEscherichia coliand the distribution of the colistin resistance genemcr-1.1in the plasmid population. |
| Databáze: |
OpenAIRE |
| Externí odkaz: |
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