Changes in Version 9

Major Changes

• Updated Java runtime environment to open-source version 17 that among many other improvements brings better support for high resolution displays.
• Redesigned and easier installation of Windows Subsystem for Linux (WSL) and bioinformatic tools for Linux OS.
• New Chromosome and Plasmids Overview Task Template for plasmid reconstruction and characterization using MOB-suite (requires WSL update).
• New CGE MobileElementFinder Task Template (requires WSL update) for detection of integrated mobile genetic elements (iMGEs).
• New Salmonella enterica SISTR Geno-Serotyping Task Template (requires WSL update).
• Substantial improvement of the speed of target import process from FASTA files and cgMLST.org (as of latest June 2023) queering.
• Updated NCBI AMRFinderPlus to 3.11.2 (database 2022-12-19.1).
• New long-read processing of assembled (FASTA) files with contig coverage and circularity information extraction.
• Removed submission of epidemiological metadata to cgMLST.org. All allele and optional allelic profile submissions are now anonymous only without any epidemiological metadata. Until latest June 2023 also all stored submitter data and epidemiological metadata will have been deleted from the cgMLST.org server.

Minor Changes

• Added support for SPAdes (v3.15.4) on Windows Subsystem for Linux.
• Updated CGE E. coli geno-serotyping database (CGE SerotypeFinder database version 1.0.0; 2022-05-16).
• Added support for iSeq/MiniSeq/NextSeq HD data and InterOp import .
• Added support for Illumina DNA Prep coverage specific recommendations.
• Updated shape files and city populations for geographical map function.
• Added support for processing NCBI gbff files (including extraction of circularity information).
• Added support for extraction of circularity information from NCBI Genome data.
• Added support for multiple fasta files in Tools menu function Mash Identification.
• Fixed handling of near identical species (e.g., E.coli/Shigella) in contamination check and automatic project selection.
• Added support for PacBio/Oxford Nanopore coverage specific recommendations.
• Added import for PacBio run infos (beta).
• Added column for amino acid position number (AA Number) to group specific SNVs result table.
• Updated FastQC to version 0.11.9.
• Added exportable MST Cluster table to MST Statistic function.
• Improved field choosing for CSV export in pipelines to export results in other tools (e.g., for customized reports).
• Fixed ST field detection for some legacy MLST task templates.
• Added option to export of contig files to keep original contig names.
• Enabled target QC start/stop codon check in some public cgMLST task templates, if they were downloaded with version 7/8 (A. baumanni, B. melitensis, E. faecalis, E. faecium, F. tularensis, L. monocytogenes, M. gallisepticum). For other species the check was already enabled and nothing has changed.
• Added storing of contig name and position for VFDB results.
• Added seed genome annotations column to allele result table of cgMLST task entries (not shown by default).
• Allowed editing of Task Template Result Field Definitions.
• Added Server status window to start and stop a SeqSphere+ server that was installed as Windows Service.
• Some further small improvements and bug fixes.

See complete version history for minor version changes and older versions see.