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This collection of tools, Bayesian Estimated Core Genome Tools, is intended to provide a simple pipeline for calculating the estimated core genome of a set of genome sequences, based on the output obtained from Genome Comparator [1]. As well as calculating the estimated core genome, tools are also provided for the calculation of median pairwise distances for alignments generated by Genome Comparator for each gene based on the reference genome. Finally, there is a tool for generating the necessary files to create the genome diagrams seen in van Tonder et al. [2] using Circos [3].
1. Jolley KA, Maiden MC. BIGSdb: Scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 2010, 11:595.
2. van Tonder AJ, Mistry S, et al.Defining the estimated core genome of bacterial populations using a Bayesian decision model. (under review)
3. Krzywinski M, Schein J et al. Circos: an information aesthetic for comparative genomics. Genome Res 2009, 19:1639-1645.
Features
- A simple pipeline for calculating the estimated core genome of a set of genome sequences, based on the output obtained from Genome Comparator [1]
- As well as calculating the estimated core genome, tools are also provided for the calculation of median pairwise distances for alignments generated by Genome Comparator for each gene based on the reference genome. Finally, there is a tool for generating the necessary files to create the genome diagrams seen in van Tonder et al. [2] using Circos [3].
- 1. Jolley KA, Maiden MC: BIGSdb: Scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 2010, 11:595.
- 2. van Tonder AJ, Mistry S, Bray JE, Hill DMC, Cody AJ, Farmer CL, Klugman KP, von Gottberg A, Bentley SD, Parkhill J, Jolley KA, Maiden MCJ, Brueggemann AB. Defining the estimated core genome of bacterial populations using a Bayesian decision model. (under review)
- 3. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA: Circos: an information aesthetic for comparative genomics. Genome Res 2009, 19:1639-1645.