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Updated: Feb 12, 2026

Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics'
Published on: May 26, 2013
Genome-by-genome approach for fast bacterial genealogical relationship evaluation
Ji Zhang1, Yanwen Xiong2, Lynn Rogers1
1mEpiLab, New Zealand Food Safety Science & Research Centre, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand.
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.
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