Tool to refine cg/wgMLST Schemas

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  • License: GNU General Public License v3 (GPLv3) (GNU GENERAL PUBLIC LICENSE)
  • Author: Rita Andrade, Nuno Faria, Mykyta Forofontov, Rafael Mamede, Mário Ramirez
  • Maintainer: UMMI
  • Tags bioinformatics , genomics , mlst , bacteria , cgmlst , wgmlst , outbreak detection , allele calling , bacterial typing , bacterial genome analysis
  • Requires: Python >=3.9
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Project description

SchemaRefinery - A Tool for Refining Genomic Schemas

For a more detailed description of the functionalities available in Schema Refinery refer to SchemaRefinery documentation

Description

Schema Refinery is a comprehensive toolkit designed for refining and managing MLST schemas. It provides a suite of modules for various tasks such as selecting and downloading genome assemblies for schema creation, identifying paralogous and spurious loci, annotating schema loci, and adapting loci sets into standardized schemas.

News

Version 0.4.0 - 2025-07-31

  • Optimized all modules to improve efficiency and the accuracy of the results.
  • Restructured output files to improve readability and simplify parsing.
  • Fixed several issues.

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Avatar for MForofontov from gravatar.com MForofontov Avatar for RAndrade from gravatar.com RAndrade Avatar for rfm from gravatar.com rfm

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Project links
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  • License: GNU General Public License v3 (GPLv3) (GNU GENERAL PUBLIC LICENSE)
  • Author: Rita Andrade, Nuno Faria, Mykyta Forofontov, Rafael Mamede, Mário Ramirez
  • Maintainer: UMMI
  • Tags bioinformatics , genomics , mlst , bacteria , cgmlst , wgmlst , outbreak detection , allele calling , bacterial typing , bacterial genome analysis
  • Requires: Python >=3.9
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0.5.0

This version

0.4.0

0.3.3.1

0.3.2.4

0.3.1 yanked

Reason this release was yanked:

Numpy and pandas version incompatible

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