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Identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. Gubbins uses spatial scanning statistics to identify loci containing elevated densities of base substitutions suggestive of horizontal sequence transfer. Gubbins is also a practical tool in the context of current sequencing capacity; it is typically able to converge on a result for an alignment of 100 two megabase sequences in well under an hour, whereas others sophisticated model fitting can take weeks to analyze a much smaller number of genomes.

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Gubbins versioning

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Gubbins classification

Gubbins specifications

Software type:
Package/Module
Restrictions to use:
None
Output format:
EMBL, GFF3, VCF, CSV, FASTA, PHYLIP, TRE
Programming languages:
C, Python
Computer skills:
Advanced
Stability:
Stable
Source code URL:
https://github.com/sanger-pathogens/Gubbins
Debian:
https://packages.qa.debian.org/g/gubbins.html
Interface:
Command line interface
Input data:
A whole genome alignment with polymorphic sites.
Operating system:
Unix/Linux
License:
GNU General Public License version 2.0
Version:
2.2.0
Maintained:
Yes
Conda:
https://bioconda.github.io/recipes/gubbins/README.html
Issue URL:
https://github.com/sanger-pathogens/Gubbins/issues

Gubbins support

Maintainer

  • Simon Harris <>

Credits

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Publications

Institution(s)

Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Center for Communicable Disease Dynamics, Harvard School of Public Health, Boston, MA, USA; Department of Infectious Disease Epidemiology, Imperial College London, St. Mary’s Campus, London, UK; Cardiff School of Biosciences, Sir Martin Evans Building, Cardiff, UK; School of Computing, Engineering and Mathematics, University of Brighton, Brighton, UK; Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge, UK

Funding source(s)

This work was supported by Wellcome Trust [098051].

Link to literature

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