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Method: Accurate and fast graph-based pangenome annotation and clustering with ggCaller
- Samuel T. Horsfield,
- Gerry Tonkin-Hill,
- Nicholas J. Croucher,
- and John A. Lees
Genome Res. September 2023 33: 1622-1637; Published in Advance August 24, 2023, doi:10.1101/gr.277733.123
...genes, more than 5000 accessory genes) (Corander et al. 2017). Escherichia coli is a genetically diverse enteric bacterium, with an intermediate-size core , but extensive accessory (approximately 3000 core genes, more than 100,000 accessory genes) (Park et al. 2019). These three species are important...
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Method: Fast and flexible bacterial genomic epidemiology with PopPUNK
- John A. Lees,
- Simon R. Harris,
- Gerry Tonkin-Hill,
- Rebecca A. Gladstone,
- Stephanie W. Lo,
- Jeffrey N. Weiser,
- Jukka Corander,
- Stephen D. Bentley,
- and Nicholas J. Croucher
Genome Res. February 2019 29: 304-316; Published in Advance January 24, 2019, doi:10.1101/gr.241455.118
..., such as Escherichia coli, Salmonella enterica, and Staphylococcus aureus (Fig. 4; Supplemental Fig. S5). These exhibited much stronger evidence of deep population structure, characterized by multimodal between-strain distance distributions that likely reflect ancestral divergences that have not been overwritten...
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