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- Title
Genome-by-genome approach for fast bacterial genealogical relationship evaluation.
- Authors
Zhang, Ji; Xiong, Yanwen; Rogers, Lynn; Carter, Glen P; French, Nigel
- Abstract
Motivation Large-scale whole-genome sequencing dataset-based studies are becoming increasingly common in pathogen surveillance and outbreak investigations. A highly discriminative and time-efficient bioinformatics tool is needed to transform large amounts of sequencing data into usable biological information. To replace the intuitive, yet inefficient, way of gene-by-gene allele calling algorithm, a new algorithm using genome-by-genome approach was developed. Results Tests showed that the program equipped with the new algorithm achieved significant improvements in allele calling efficiency compared to a conventional gene-by-gene approach. The new program, Fast-GeP, rendered a fast and easy way to infer high-resolution genealogical relationships between bacterial isolates using whole-genome sequencing data. Availability and implementation FAST-GeP is freely available from: https://github.com/jizhang-nz/fast-GeP. Supplementary information Supplementary data are available at Bioinformatics online.
- Subjects
GENEALOGY; BACTERIAL communities; ALGORITHMS; GENOMES; NUCLEOTIDE sequencing
- Publication
Bioinformatics, 2018, Vol 34, Issue 17, p3025
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/bty195