Bacterial Genomics Group: Methods development papers

QuantTB - a method to classify mixed Mycobacterium tuberculosis infections within whole genome sequencing data.

1.PubMed Google Scholar DOI

Anyansi C, Keo A, Walker BJ, et al. QuantTB - a method to classify mixed Mycobacterium tuberculosis infections within whole genome sequencing data. BMC Genomics. 2020;21(1):80. doi:10.1186/s12864-020-6486-3.

Computational Methods for Strain-Level Microbial Detection in Colony and Metagenome Sequencing Data.

1.PubMed Google Scholar DOI

Anyansi C, Straub TJ, Manson AL, Earl AM, Abeel T. Computational Methods for Strain-Level Microbial Detection in Colony and Metagenome Sequencing Data. Front Microbiol. 2020;11:1925. doi:10.3389/fmicb.2020.01925.

ProphET, prophage estimation tool: A stand-alone prophage sequence prediction tool with self-updating reference database.

1.PubMed Google Scholar DOI

Reis-Cunha JL, Bartholomeu DC, Manson AL, Earl AM, Cerqueira GC. ProphET, prophage estimation tool: A stand-alone prophage sequence prediction tool with self-updating reference database. PLoS One. 2019;14(10):e0223364. doi:10.1371/journal.pone.0223364.

SynerClust: a highly scalable, synteny-aware orthologue clustering tool.

1.PubMed Google Scholar DOI

Georgescu CH, Manson AL, Griggs AD, et al. SynerClust: a highly scalable, synteny-aware orthologue clustering tool. Microb Genom. 2018;4(11). doi:10.1099/mgen.0.000231.

Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.

1.PubMed Google Scholar DOI

Walker BJ, Abeel T, Shea T, et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One. 2014;9(11):e112963. doi:10.1371/journal.pone.0112963.