kjolley/BIGSdb: Version 1.51.6

This release adds two new analysis plugins and other improvements:

• New GeneScanner plugin
• New PlasmidFinder plugin
• Updates to various plugins to support analysis fields (third-party results stored as JSON within the database)
• Improved performance for searchable locus lists
• Added retries on database queries if network errors are encountered.
• Included more locus information in the API to facilitate database synchronisation/cloning via the API

GeneScanner

This tool performs a mutation analysis on sequences aligned from genome assemblies in the database for a selected locus or an uploaded gene/protein sequence. The tool is described in Kobras et al. 2025 bioRxiv 2025.11.02.685864. To enable GeneScanner it first needs to be installed and then set the genescanner_path in bigsdb.conf, e.g.

genescanner_path=/home/bigsdb/genescanner/.venv/bin/python3 /home/bigsdb/genescanner/GeneScanner/mutation_analysis.py

PlasmidFinder

This plugin is a wrapper for the PlasmidFinder tool described in Carattoli et al. 2020 Methods Mol Biol 2075:285-294. It can run PlasmidFinder against one or more isolates and output the results in a table and as JSON files. In addition, if plasmids are identified then the JSON output is stored within the database for future use and the results are included with an isolate record in tabular format. There is also a stand-alone script to run PlasmidFinder against one or all databases so that the results can be generated and stored from a scheduled job.

PlasmidFinder needs to be installed as a Docker image and enabled in bigsdb.conf, e.g.

Other improvements

Full Changelog: https://github.com/kjolley/BIGSdb/compare/v_1.51.5...v_1.51.6