Changes in Version 10

Major Changes

• New storage of all NCBI AMRFinderPlus results (e.g., also disinfectans or metals) in SeqSphere database fields and update to version 3.11.26 (database 2023-11-15.1).
• New export functions for sequences from NCBI AMRFinderPlus and MobileElementFinder (iMGEs) results.
• New Long-read Data Plasmid Transmission Analysis Module (part of the extra charged Long-read Data Analysis Bundle [LDAB]).
• New ONT Data Assembly Module (beta; part of LDAB).
• New interactive fix start and orientation of (circular) chromosomes and plasmids by using dnaA and rep targets, respectively.
• New interactive comparison and visualization of (annotated) plasmids and chromosomes using pyGenomeViz.
• New automatic import of sample metadata from CSV file(s) during pipeline processing.
• New summary and plasmids statistics in Sample QC Overview.
• Revised species identification and improved E. coli / Shigella discrimination.

Minor Changes

• Updated Mash reference database used for species identification and contamination check (now containing 30,547 genomes from NCBI).
• Updated MOB-suite to 3.1.8 and storage of replicon positions in database.
• New option to disable MOB-recon in pipeline and in manual processing.
• Updated CGE MobileElementFinder to 1.1.2.
• New Default Metadata Fields that are defined on project level are now not only shown in comparison tables but also in clonal and plasmid early warnings and search similar samples and plasmid search results.
• New pipeline script feature to choose multiple projects at once via projects selection button.
• New pipeline script feature to use same assembler settings as for the first project when working with multiple species.
• Pipeline script advanced setting 'Only process samples that do not exist in projects' now checks for all projects of the pipeline.
• Reprocessing pipelines now support tag operators (all, any, none) and can set tags for parallel re-processing of samples in a project.
• New project name column in comparison tables and as exportable field in metadata export.
• New genotyping result state (e.g., error or succeed) column in comparison tables and in database search.
• Fixed export of custom date fields in comparison table.
• New next/prev button to stay in same task template of different samples in the navigation pane.
• New project organism field with tooltip from which task template(s) the species information was derived.
• Changed behavior of SeqSphere Server service on MS Windows during reboot.
• New support for gbff files as seed genome in the cgMLST Target Definer tool.
• Fixed a problem with ENA submissions when no genus or species is specified.
• Updated NCBI SRA Toolkit to 3.0.10 to solve problems when downloading newer FASTQ files.
• Adapted PacBio run info import to changes in SMRTLink V13.0 update.
• Improved installation of bioinformatic tools under Linux by using micromamba.
• Preventing splash image showing in Linux command line mode.
• New option to copy & paste color values in comparison table group color windows.
• New option to show in minimum spanning trees the connection lines with distances between selected nodes (in contrast to all nodes).
• New support to start GrapeTree as external application for visualization of very large datasets.
• New interactive multi-project import of sample metadata.
• New epi metadata import now allows to clear existing values in database by importing empty cells.
• Fixed a problem in pipeline mode with special characters in filenames.
• Some further small improvements and bug fixes.

For older versions see complete version history.