Changes in Version 10.5

Major Changes

• New proactive vulnerability assessment with fixing of several issues (all were non-critical) in preparation for the EU Cyber(security) Resilience Act.
• New support for authentication of BIGSdb/pubMLST Oxford and Pasteur that is required to retrieve MLST alleles, STs, and schemes generated after 31.12.2024.
• Updated NCBI AMRFinderPlus to version 4.0.15 with database 2024-12-18.1 (changes).
• Updated Salmonella enterica geno-serotyping tool SISTR to version 1.1.3 with additional QC messages (changes).
• Updated ONT Data Assembly Module to automatically handle MinKNOW output including sample sheet function and storage of run details (part of LDAB).
• New ONT-cgMLST-Polisher for tertiary polishing of ONT assemblies (part of LDAB).
• Updated Medaka to version 2.0 with bacterial methylation model (part of LDAB).
• New tutorial for assembly of Oxford Nanopore MinKNOW sequencing data (part of LDAB).

Minor Changes

• Released cgMLST task templates for Enterobacter hormaechei, Morganella morganii, and Proteus mirabilis.
• Removed stop codon check for C. jejuni/coli cgMLST and Accessory task templates to improve perc. good cgMLST targets for C. coli samples.
• Removed outdated VFDB task templates and added a tutorial on how academic users can create/update them manually.
• New function to set password policy added.
• New increased length of result fields to store long list of resistance/virulence targets.
• New plasmid clustering function added to plasmid database and alert view.
• New distance matrix export function added to plasmid database view.

• Improved minimum spanning tree layout.
• New further distance threshold for invisible connection lines added to Minimum Spanning Tree.
• New radial equal-daylight layout for phylogenetic trees added.
• New manual function for creating a plasmid distance MST based on exported plasmid distance matrix added.

• New option to automatic remove empty columns in comparison tables added.
• Improved performance for metadata import and for setting values in comparison table.
• Renamed Find Value command in comparison table menu into Search in Comparison Table.

• Improved pipeline script editor for multiple projects.
• New support of multiple positions for a Sample ID in pipeline script file naming section.
• New pipeline mode command line parameter -t for thread count added.
• New deterministic option for ONT data assembling pipelines for QC added.

• New database maintenance and recovery function to export/import data from damaged database files added for admin(s).
• New history function for reusing previous database searches added.
• New support for regular expression in database searches added.
• New dialog for managing sample tags added.
• New option to table export dialogs to copy table directly to clipboard added.

• New button to adjust access control for multiple projects at once to project manager dialog added.
• New contig/SPEC export function with the option to use project acronyms as sub-folder names, instead of full project names added.
• New mark for outdated/deprecated task templates added.

• New option to filter SNV result table by differences in specific samples added.
• Updated instruments in ENA upload and fixed some field validation problems.
• Removed outdated submission to ECDC (TESSy).
• Some further small improvements and bug fixes.

For older versions see complete version history.