Version 10.0.2 (03-Jun-2024)

    Minor Changes
  • Updated Illumina InterOp utilities to 1.3.1 for reading NextSeq 1k/2k data.
  • Fixed logout dialog behaviour when tasks are running in background.
  • Fixed GUI issue in manual backup function.
  • Fixed XLSX export of table cells with colored foreground.
  • Fixed issue with bioinformatic tools installation on Linux OS.
  • Changed download-URL for Ridom WSL distribution.
  • Fixed bug when using parenthesis with GrapeTree.
  • For pyGenomeViz, check gb/gbff-files for dna sequences.
  • Fixed error that metadata.csv was not found.
  • Fixed issue with unzipped ONT FASTQ files.

Version 10.0.1 (06-May-2024)

    Minor Changes
  • Server only: Fixed issue when updating the Windows Service on some systems.
  • Server only: Fixed issue for large sketches in Mash Plasmid Typing (Long-read Data Plasmid Transmission Analysis Module).

Version 10.0.0 (22-Apr-2024)

    Major Changes    Minor Changes

Version 9.0.13 (27-Oct-2023)

    Minor Changes
  • Server: Experimental update with HSQLDB 2.7.2.

Version 9.0.11/12 (20-Sep-2023)

    Minor Changes
  • Server: Changed database settings for newly created databases.

Version 9.0.10 (07-Sep-2023)

    Minor Changes
  • Updated ENA submission for changed validation checks of field 'geographic location (country and/or sea)'.
  • Improved behaviour when a Windows computer is shutdown without exiting SeqSphere server or client.
  • Changed QC coloring for PacBio coverage (new green threshold ≥40).
  • Changed QC coloring of top matching species.
  • Fixed comparison table function for deleting of specific values in database.
  • Fixed issue with adapter trimming of four FASTQ files.
  • Fixed unicode handling of WSL output.
  • Reduced frequency of pipeline reports for continuous pipelines.
  • Added database checkpoints before starting backups.
  • Added summary table to sample QC Overview.
  • Added for Mash functions in tools menu support for network drives.

Version 9.0.9 (14-Jul-2023)

    Minor Changes
  • Fixed fwd/rev FASTQ file naming detection.
  • Fixed issue with contig names in BAM files.
  • Fixed issue when reading xslx files with high compression.
  • Fixed issue in SNV export to FASTA file.

Version 9.0.8 (15-Jun-2023)

    Minor Changes
  • Added cgMLST allelic profile submission button to sample search result panel.
  • Fixed issue with SPAdes and Chromosome and Plasmid Overview.

Version 9.0.7 (09-Jun-2023)

    Minor Changes
  • Fixed issue with miGenomeSurv submission.
  • Added timeout for initialisation of login session.

Version 9.0.6 (07-Jun-2023)

    Minor Changes
  • Updated ENA submission for changed validation checks: 'collection date' is now mandatory, and 'country' is now mandatory and submitted to'geographic location (country and/or sea).
  • Prevent waiting for missing network drives in procedure panel.

Version 9.0.5 (02-Jun-2023)

    Minor Changes
  • Fixed miGenomeSurv download for projects with two E. coli cgMLST schemes.

Version 9.0.4 (24-May-2023)

    Minor Changes
  • Fixed gui-less mode for FastQC when starting SeqSphere in Linux environment without display.

Version 9.0.3 (15-May-2023)

    Minor Changes
  • Support installation of Linux tools for anaconda/mambaforge/miniforge.
  • Improved support for X2Go environments.
  • Fixes and error when exporting large colored tables to files.
  • Show WSL version selection box also for Windows 10 / Windows Server.

Version 9.0.2 (27-April-2023)

    Minor Changes
  • Solves installation problems on Windows Server 2019.
  • Fixes an error in SISTR typing for some data.
  • Fixes an error in MOB typing when reprocessing some old data.
  • Fixes an error when adding samples to comparison table after adding new columns to it.
  • Changed predefined ONT procedure details.

Version 9.0.1 (20-April-2023)

    Minor Changes
  • Fixes in reprocessing pipelines an error for samples without cgMLST tasks when performing EWA.
  • Fixes plasmid contig export for truncated contig names.

Version 9.0.0 (11-April-2023)

    Major Changes    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 import and InterOp.
  • Added support for Illumina DNA Prep coverage specific recommendations.
  • Updated shape files and city populations for geographical map function.
  • Added support for processing 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.
  • 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.

Version 8.5.2 (01-Feb-2023)

    Minor Changes
  • Fixed headless mode when starting client in Linux environment without display.

Version 8.5.1 (28-Nov-2022)

    Minor Changes
  • Fixed wrong species contamination warnings between Shigella and E. coli.

Version 8.5.0 (23-Nov-2022)

    Minor Changes
  • Revised download of NCBI genomes.
  • Revised download of SRA metadata.
  • Revised metadata CSV export in pipeline.
  • Revised tree export to EMF and SVG files.
  • Added support for BGI sequencer data.
  • Added shortcuts in right-click menu of ‘Processed Assembled Genome Files' function to open or delete existing samples.
  • Update SPAdes to version 3.15.4.
  • Revised search Sample ID operator 'in list' in sample search dialog.
  • Fixed issue for importing Mycobacteria MLST task template.
  • Changed initial target QC setting when importing new MLST task templates.

Version 8.4.2 (26-Sep-2022)

    Major Changes
  • Updated NCBI SRA Toolkit to solve problems when downloading FASTQ files.
    Minor Changes
  • Added Consortium server check to system test.

Version 8.4.0/1 (09-Sep-2022)

    Minor Changes
  • New function for allele nomenclature inconsistency check.

Version 8.3.5 (07-Jul-2022)

    Minor Changes
  • Adapted SRA download function to NCBI site changes.
  • Removed NZ_AP020315 from Mash reference database to prevent wrong classification of S. argenteus samples.
  • Improved support for smaller screen resolutions.
  • Fixed missing average coverage value for high coverage data and pipelines without downsampling.

Version 8.3.4 (15-Mar-2022)

    Minor Changes
  • Ignore and overwrite '?' as SLC ID if clustering is perforemd (requires server update).
  • Export missing values in comparison as empty value by default (can be changed in export with button 'Missing Values...').
  • Catch wrong window sizes when exporting MST.

Version 8.3.3 (25-Feb-2022)

    Minor Changes
  • Added SARS-Cov-2 Nimagen v4.02 bed file.
  • Added export function for Early Warning Alert table.
  • Revised localhost detection in proxy usage.
  • Fixed issue in WSL detection.
  • Fixed format checking issue of when importing some Excel files.

Version 8.3.2 (03-Feb-2022)

    Minor Changes
  • Additional logging in debug mode.

Version 8.3.1 (01-Feb-2022)

    Minor Changes
  • Fixed issue in SLC and EWA settings dialog.

Version 8.3.0 (21-Jan-2022)

    Major Changes    Minor Changes
  • Numeric sorting in comparison table and MST legend of ST, CT, spa-types, etc.
  • Improved report of updated MLST results after updating MLST task templates.
  • Updated pangolin task template fields to store additional version info (task template update can be downloaded in SeqSphere).
  • Added SARS-Cov-2 ARTIC v4 bed file.
  • Added SARS-Cov-2 for Nimagen kit autocorrection of wrong read mapping at del 60-70 for Omicron variant.
  • Exclude spa-types with less than 5 repeats from distance calculation (according to original BURP publication).
  • Added date format check of values before starting epi metadata import.
  • Fixed issue with Newick file export of MST clusers.
  • Fixed issue with Sample report introduced with version 8.2.
  • Modified Linux start script to support symbolic links.
  • Some further small improvements and bug fixes.

Version 8.2.0 (20-Dec-2021)

    Major Changes
  • Updated log4j library to version 2.17 to address CVE-2021-44228.
  • Updated NCBI SRA URL to solve problems when downloading FASTQ files.
    Minor Changes
  • Support more than two read files for adapter trimming.
  • Revised and faster retrieval of samples for comparison table.

Version 8.1.0 (04-Nov-2021)

    Major Changes
  • New functionality for a SeqSphere+ Consortium that allows several SeqSphere+ users each with their own installation to share a minimum agreed upon amount of data (e.g., for [supra]national/regional genomic surveillance or in the framework of a funded project, etc.) while the original and complete data remain locally.
  • Revised spa-typing task template for improved detection of spa-types from WGS data. Possibility to submit new spa-types with known spa-repeats from WGS data to SpaServer (new spa-repeats still need confirmation by Sanger sequencing).
  • New postfixes in AMRFinderPlus task template now appending ESBL, ampC, and carbapenemase for class BETA-LACTAM in the result fields.
    Minor Changes
  • New function to assign tags to samples in a comparison table.
  • Changed order of task templates in comparison tables that are created from multiple projects.
  • Fixed that samples with a SLC ID that are moved to another project get the SLC ID either deleted (new project without SLC IDs) or newly determined (new project with SLC IDs).
  • Fixed AMRFinderPlus organism setting for Campylobacter if Mash identification is not performed.
  • Export profile and metadata files for GrapeTree.
  • Some further small improvements and bug fixes.

Version 8.0.2 (02-Sep-2021)

    Minor Changes
  • Provide newly created SLC IDs to already existing comparison table snapshots (server only).

Version 8.0.1 (23-Aug-2021)

    Minor Changes
  • Fixed issue when updating old SARS-CoV-2 task template.
  • Fixed issue with SRA download test in system test.

Version 8.0.0 (17-Aug-2021)

    Major Changes
  • New Sample QC Overview that allows for user selected samples to create a table that summarizes all QC parameters for those samples. Similar summaries are now shown also in the Pipeline Report and Sequencing Run Details.
  • New recursive similarity searches now possible. If a recursive search is performed, all samples that are within the defined allelic threshold to any hit samples are returned also. This is repeated until no additional hit samples are found.
  • New project specific Early Warning Alerts (EWA) for detecting and noting sample clusters automatically replaces Cluster Alerts. EWAs can be defined for various projects separately and multiple EWAs with different allele thresholds and/or metadata criteria (e.g., location, date, etc.) can be defined per project.
  • New project specific Local Single Linkage Clustering IDs can be assigned according to cgMLST profiles of samples automatically. This allows to build a sort of 'nomenclature' based just on own samples only. Local SLCs IDs can be defined for various projects separately and multiple hierarchical Local SLC IDs can be defined per project.
  • New function to find and mark columns in Comparison Table that makes gene and product annotations searchable (Comparison Table menu Edit | Find Column).
    Minor Changes
  • Updated NCBI AMRFinderPlus to version 3.10.5 with among others an increased number of species supported for screening of point mutations.
  • Improved selecting and adding of genotyping schemes for distance calculation in Comparison Table (Comparison Table menu Columns | Select Genotyping Schemes for Distance Calculation).
  • Two new Comparison Table functions Data | Add Additional Samples to Table by Allelic Similarity or ... with Same SLC ID.
  • New numeric sorting of number only columns in Comparison Table for correct sorting of those columns (previously alpha-numeric).
  • Find Group Specific SNVs and Find SNVs searches improved for non-seed genome targets.
  • More flexible handling of repeatedly sequenced samples.
  • Sample tags can now be searched with boolean expressions in the advanced mode of the search.
  • Export CSV files in pipeline for each processed sample with configurable metadata. Thereby, SeqSphere+ results can be automatically imported in other tools.
  • Setting of genus and species database fields of Sample automatically according to Mash result (previously taken statically from the cgMLST Task Template).
  • SARS-CoV-2 pangolin task template and server updated to handle and show Scorpio results (including WHO label).
  • Some GUI revisions, smaller improvements, and bug fixes.

Version 7.8.0 (01-Jul-2021)

    Minor Changes
  • Added scorpio fields to pangolin result.
  • Added further predefined bed files.
  • Fixed number format for excel file export.

Version 7.7.5 (02-Jun-2021)

    Minor Changes
  • Fixed linking of SKESA BAM files when writing them to external directory.

Version 7.7.4 (31-May-2021)

    Minor Changes
  • Minor improvements for GISAID import and submission.
  • Fixed storing of default comparison table fields for projects.

Version 7.7.2 (27-May-2021)

    Minor Changes
  • Removedtoolbar from project comparison table.
  • Fixed task template updating issue while samples are loaded.

Version 7.7.0 (25-May-2021)

    Major Changes
  • Changed iVar pipeline parameters: Minimum frequency threshold to call consensus was set 70% (-t 0.7).
  • Variant read frequency and total coverage at variant positions are shown for variants found in iVar pipeline.
    Minor Changes
  • New procedure statistics QC fields in iVar pipeline: Low frequency variants (genome wide), Variants (genome wide), Consensus Bases with Non-N Ambiguity.
  • Coverage plot can be inspected with Broad's Integrative Genomics Viewer (IGV) for read level QC.
  • New general procedure statistics field: GC-Content.
  • Fixed storing of MST distance in stored comparison table retrievals.

Version 7.6.1 (03-May-2021)

    Major Changes
  • New export function for sequences and metadata for batch-upload to GISAID.
  • New import function for sequences and metadata downloaded from GISAID.
  • New export of samples into a multiple FASTA file (e.g., for visualization with Nextclade).
    Minor Changes
  • Specific genome positions can be inspected with Broad's Integrative Genomics Viewer (IGV) for read level QC.
  • Changed iVar pipeline parameters: Samtools mpileup maximum depth (-k) set to 1,000,000 for better support of regions with high coverage (Parameter is changed automatically in existing pipeline scripts).
  • Changed SARS-CoV-2 database schema: Added 'Sampling Strategy', 'Nextstrain Clade', 'GISAID Clade', 'Ct Value'. Removed 'GISAID Download' tab fields and some 'Epi Characteristic' fields.
  • Replaced field 'Perc. Consensus Bases Below Coverage Threshold' with absolute value field 'Perc. Consensus Bases Below Coverage Threshold (Ns)'.
  • Allow offline installation of iVar on WSL.

Version 7.5.5 (09-Apr-2021)

    Minor Changes
  • Fixed issue for E. coli serotyping.
  • Fixed storing of MST cluster threshold in comparison table snapshots.
  • Fixed downsampling issue.
  • Allow to assign base edits to procedure assembly files.

Version 7.5.4 (30-Mar-2021)

    Minor Changes
  • Allow exporting BAM files in SARS-CoV-2 pipeline.
  • Improved autodetection of iVar and Samtools application paths on Linux.
  • Show absolute position in window status bar.

Version 7.5.3 (23-Mar-2021)

    Minor Changes
  • Added for virus: QC field for percentage of consensus bases below coverage threshold.

Version 7.5.2 (22-Mar-2021)

    Minor Changes
  • Fixes consensus calling problems for mappings with high coverage.
  • Fixes calculation of average coverage.

Version 7.5.1 (17-Mar-2021)

    Minor Changes
  • Fixes a problem with some projects in pipeline script editor.

Version 7.5.0 (15-Mar-2021)

    Major Changes
  • SARS-CoV-2 Analysis with task templates for detection of notable mutations, PANGO lineage typing, and Illumina tiled amplicon pipeline.

Version 7.2.5 (07-Dec-2020)

    Minor Changes
  • Configurable WSL app path and revised automatic WSL detection.
  • Allow to define in spa-typing task template own file naming conventions.
  • System Test function in Help menu.
  • Evaluating approximated genome size also for FASTA input data.
  • Some smaller improvements and bug fixes.

Version 7.2.4 (09-Oct-2020)

    Minor Changes
  • Adapted FTP client to ENA server changes.
  • Fixed proxy connection problem for Basic Authentication.
  • Fixed detection of already existing NCBI AMRFinderPlus task entries in pipelines.
  • Allow Task Template specific configuration of BLAST version.
  • Some smaller improvements and bug fixes.

Version 7.2.3 (07-Sep-2020)

    Minor Changes
  • Fixed scanning problem for WGS spa-typing.
  • Increased connection timeout for queries to cgMLST.org.

Version 7.2.2 (01-Sep-2020)

    Minor Changes
  • Fixed Windows Subsystem for Linux detection problem on Windows Server 2019 systems.

Version 7.2.1 (17-Aug-2020)

    Minor Changes
  • Only the first given species of a sample is now used for submissions to ENA.
  • File copy retry option in advanced settings of Pipeline Script.

Version 7.2.0 (30-Jul-2020)

    Major Changes
  • New spa-typing task template for sanger sequencing and WGS data (requires also server update).
    Minor Changes
  • Updated Mash reference database used for identification and contamination check (now containing 18,184 genomes from NCBI).
  • Improved NCBI download of WGS assemblies in 'Process Assembled Genome Data' function.
  • Support for Ubuntu 20.04 as Windows Subsystem for Linux (WSL).
  • Some GUI revisions, smaller improvements, and bug fixes.

Version 7.1.0 (08-Jun-2020)

    Minor Changes
  • Support in by Browsing NCBI Bacteria Genome Browser NCBI Genome browser for downloading chromosomes and plasmids together into a single sample or file. Changed genome data set NCBI Browser for arbitrary value in result field lookup tables (required for C. perfringens Toxinotyping).
  • Support for arbitrary value ('*') in result field lookup tables (required for C. perfringens Toxinotyping).

Version 7.0.6 (27-May-2020)

    Minor Changes
  • Fixed thread settings in SPAdes and SKESA for computers with more than 100 cores.
  • Support for fasta.gz and gb.gz in cgmlst target definer.

Version 7.0.5 (25-May-2020)

    Minor Changes
  • By default, the clustering in minimum spanning trees is now only enabled for trees based on cgMLST only.
  • Export Sample Contig and SPEC Files dialog slightly changed in epi metadata filter settings.
  • AMRFinderPlus: removed green highlighting for Virulence result rows, as they are not stored as result fields.
  • Fixed PDF file creation for sample reports.
  • Setting approx. genome size for NCBI GenBank files in procedure details.

Version 7.0.4 (04-May-2020)

    Minor Changes
  • Changed concatenating for multi copy genes in VFDB and AMRFinderPlus.

Version 7.0.3 (29-Apr-2020)

    Major Changes
  • New virulence profiling task templates for 54 species with medical importance based on the Virulence Factor Database (VFDB).
  • New E. coli O- and H-antigen serotyping task template based on the CGE SerotypeFinder database.
  • New task template for all currently supported species except MtbC for antimicrobial resistance gene finding based on the NCBI AMRFinderPlus tool and database (requires Linux or Windows Subsystem for Linux on Windows 10 / Windows Server 2019 [WSL]).
  • Reference mapping pipelines use by default in new scripts the 3-4 times faster BWA-MEM algorithm instead of BWA-SW. Both algorithms produce rarely small allelic differences (1-2 alleles) and occasionally a slightly different number of found targets (requires Linux or WSL).
  • By default improved speed for larger seed genomes (>= 6 Mbases; no public cgMLST scheme at the time-point of this release has a seed genome of this size) in target scanning step. External BLAST+ version is used instead of our internal BLAST tool for those genomes to improve speed. The effect is especially pronounced on computers with more than 4 cores or genomes larger than 7 Mbases. BLAST+ and BLAST will not produce any allelic differences but in some samples the two algorithms can produce a slightly different number of found targets.
  • Shortcut function in comparison table creation dialog for storing selected fields as project, general, or system defaults for metadata fields shown in comparison table and exported fields of samples.
  • Support for Illumina adapter trimming with Trimmomatic directly in pipelines.
  • Support for FastANI via tools menu for fast computation of whole-genome ANI (Average Nucleotide Identity) to estimate the similarity to a reference genomes and to define species boundaries (requires Linux or WSL).
  • GC content change filter and column in Group Specific SNP result table for better support of high-resolution melting curve (HRMC) assays.
    QC Improvements
  • Remapping of reads by default with BWA and consensus calling as polishing step for SKESA and SPAdes de novo assemblies. As SPAdes is known to create inaccurate alignments for data with low coverage by default a minimum base coverage of 5 is required to call a non-ambiguous base. For SKESA no minimum coverage is applied by default as it already uses more conservative heuristics than SPAdes. For more details it is referred to our updated de novo assembler evaluation documentation.
  • Consensus caller for BWA reference mapping in new pipelines scripts now requires by default a minimum base coverage of 5 to call a non-ambiguous base, if the estimated average coverage (unassembled) is below 50. If the average coverage is above 50 no minimum coverage is applied.
  • New default Start/Stop codon check in target QC of all cgMLST and Accessory task templates. If enabled (check cannot be disabled in public schemes) the check fails if no start codon is found at the begin, no stop codon is found at the end, or a stop codon is found at a wrong position in a target. Therefore, re-analysis may produce in some samples slightly more failed targets (<1%) than previously but never different alleles.
  • Highlighting comparison table QC fields (e.g., average coverage) with traffic light colors if specific thresholds are not succeeded.
    Minor Changes
  • Export Sample Contig and SPEC Files dialog revised and possibility to filter epidemiological metadata.
  • Task Entry Overview table for resistance/virulence/geno-serotyping Task Templates (e.g., for VFDB) have a colored threshold legend, version information, and citation(s). Therefore, Task Entry Overview tables for cgMLST and MLST Task Templates are now also stated with version information and citation(s).
  • New comparison table remove columns toolbar button (with three options).
  • If the remove option is selected in Handling of Missing Values dialog (e.g., when creating MST), the columns are now removed from the comparison table instead of removing them from the distance calculation only.
  • Option to create Sample Bookmarks from samples selected in comparison table by right-click menu.
  • Layout of distance values in MST was revised to prevent overlap with connecting lines.
  • Clickable links in procedure tab of Sample Overview for Run ID and FastQC detailed results.
  • Clickable links in results tab of Sample Overview for AMRFinderPlus, VFDB, etc. detailed results.
  • Option to store NCBI Genome downloads as smaller fasta.gz files and to use in addition genus and species information in the file names.
  • Organism quick search list in NCBI Genome Browser is no longer sorted alphabetically but by the frequency of entries per species.
  • Support in NCBI Genome browser for download of 6 letter accession number draft genomes.
  • SRA download function for FASTQ files now uses NCBI SRA toolkit download as fallback strategy if the faster direct download fails.
  • Support for IBM Aspera as an alternative to FTP for uploading of FASTQs to EBI ENA. Requires the separate installation of the Aspera client by the user. Aspera uses an encrypted connection. Thereby, institutional proxy issues with FTP may be resolved (beta-version!).
  • Additional database fields 'Source Subtype' and 'ECDC Case ID' were added to Default Bacteria database scheme for support of TESSy XML-file export.
  • ECDC TESSy XML Export (beta version!).
  • Setting maximum number of threads used in general settings of pipelines.
  • Overview of citations and licenses for other programs, dynamically loaded libraries, and databases and services was revised and moved into the menu entry 'Help | Citations and Licenses'.
  • Documentation of customizing logo and welcome message.
  • Per base read coverage table for target in info button of contig view (when option store read data is enabled).
  • Option to give a reason that is stored in the task template comment when removing targets from a task template.
  • Option to clear immediately an old backup warning message in the system administration panel.
  • Bug-fix for import of phenotypic resistance data from Excel or CSV tables.
  • Default file format for export of comparison tables was changed from XLS to XLSX Excel format to support up to 16.384 columns. The export of metadata now also supports XLSX.
  • Task Template Application type 'Pathogenicity' was renamed into 'Virulence'.
  • Default setting in new pipeline scripts for submission of sample data was changed from Store only new CT founders on cgMLST.org to Store only new CT founders as anonymized samples on cgMLST.org.
  • Some GUI revisions, smaller improvements, and bug fixes.

Version 6.0.9 (25-Feb-2020)

  • Handles problems in search for similar samples.

Version 6.0.8 (21-Feb-2020)

  • Removed automatic search when adding samples to a comparison table.

Version 6.0.7 (06-Dec-2019)

  • Handles a crashed FastQC process in pipeline as warning only to prevent that the sample processing is aborted.

Version 6.0.6 (14-Nov-2019)

  • Server only: solves a problem when moving backup files to a network device mounted by a different user.

Version 6.0.5 (07-Nov-2019)

  • Solves a problem when adding fields with "," to the project comparison table default fields.

Version 6.0.4 (05-Sep-2019)

  • Backport of SRA download revision to use SRA toolkit for download.

Version 6.0.3 (05-Aug-2019)

  • Backport of SRA download improvements to solve download problems of some read data.

Version 6.0.2 (05-Jun-2019)

  • Solves parsing and download problems with some GenBank entries.

Version 6.0.1 (23-May-2019)

  • Solves a problem with missing external files (e.g. FASTQC).

Version 6.0.0 (12-Apr-2019)

  • Read data quality and adapter content control automatically possible in pipeline with FastQC. [User Guide]
  • Functionality for trimming Illumina adapters with Trimmomatic. [User Guide]
  • In the procedure tab data quality errors and warnings are shown. [User Guide]
  • Specification of project specific default epidemiological and procedure metadata fields for comparison tables. [User Guide]
  • Assessment of paired-end library insert sizes with Picard. [User Guide]
  • SKESA assembler supported to improve substantially speed of de novo assemblies (requires Linux or Windows Subsystem for Linux [WSL]). [User Guide]
  • Contamination check with Mash Screen (requires Linux or WSL). [User Guide]
  • LIMS functionality by Illumina sequencing run details (InterOp files) import in pipeline for run QC (requires Linux or WSL). [User Guide]
  • Automatic project choosing for multiple species run in pipeline with Mash Distance (requires Linux or WSL). [User Guide]
  • Improved speed when downloading scaffolds and contigs from NCBI Genomes.
  • Changed default order of task templates in new projects to sort them ascending by number of targets.
  • Often used projects can be marked as favorites. [User Guide]
  • Three additional fieldswere added to the default database scheme (v1.9): Downloaded From, Submitted To, and Case ID. [User Guide]
  • Absence of genes (allele type 0) supported in MLST typing (e.g., for E. faecium MLST).
  • Pipeline file exclusion list allows placeholder * at start and end of a file pattern and files named 'Undetermined_*' are excluded by default.
  • Sample search field criteria supports multiple values (operator 'in list') for task result fields (e.g., MLST ST).
  • Some GUI revisions, smaller improvements, and bug fixes.

Version 5.1.1 (27-Aug-2018)

  • CHANGED: Fix for ENA submission (Adaptions to changes in ENA validation checks).

Version 5.1.0 (04-Jun-2018)

  • CHANGED: Added active consent checkboxes for cgMLST.org submission and contacting us to comply with the General Data Protection Regulation (GDPR).
  • CHANGED: Improved automatic retry functionality in pipeline in case of cgMLST.org connection problems.
  • CHANGED: Switched most Internet connections to https.
  • CHANGED: Added support for SRA XML field 'Sample Title' now containing the Sample ID.
  • CHANGED: Added 'Quarter' as time scale option for the Epi Curve chart.
  • CHANGED: Fixed restore backup function for unconfigured servers.
  • CHANGED: Fixed backup setting issue.

Version 5.0.0/1 (16-Apr-2018)

  • NEW: New alleles are by default automatically assigned to cgMLST.org without sample submission.
  • NEW: Anonymized sample submission to cgMLST.org is now possible and various other submission configuration options were introduced.
  • NEW: Possibility to withdraw samples submitted to cgMLST.org was added.
  • NEW: Revised cluster-alert settings (possibility to limit the search by place and time) were added and vastly improved speed of similarity searches were implemented (now defined in a project and turned on by default for cgMLST projects).
  • CHANGED: After the Server update the database size will reduce to about 50% of the previous size by internal conversion and compression. Each newly stored sample will now only need about 5 MB storage size with default settings.
  • CHANGED: 'Cluster Type' was renamed into 'Complex Type' (static CTs that should be used for communication purposes) and MST 'Complexes' into 'Clusters' (dynamic created single linkage clustering for outbreak detection).
  • NEW: User access logging for viewing, exporting, and deleting samples was added (turned off by default, can be enabled by Administrator).
  • CHANGED: 'Reference Genome' of cgMLST Target Definer was renamed to 'Seed Genome' and 'Query Genomes' were renamed to 'Penetration Query Genomes'.
  • Changed: Default coloring of Comparison Table entries was changed to Epi Info column content by default. cgMLST 'Clusters' are by default now highlighted by shading in a Minimum Spanning tree. MST labels are now by default colored according to group color (can be disabled). New Cluster Tree Panel icon was added to the MST window and the possibility to export the cluster trees was added.
  • CHANGED: The Comparison Table functions for adding samples, adding columns, refreshing data, and storing snapshots were fixed and improved.
  • NEW: Comparison Table export allows now to specify the encoding of missing values.
  • CHANGED: The allele alignment function in the Comparison Table was improved and now supports the alignment of a larger number of samples.
  • NEW: A function to hide comment lines in MST/NJTree legend panel was added.
  • CHANGED: By default read data are not stored in targets with QC issues any more to reduce database size. However, QC messages are still preserved.
  • CHANGED: If multiple best hits are now found during target scan, all hits are imported as target sequences and the QC state is recorded as 'failed' (was previously 'not found').
  • CHANGED: SPAdes assembler was updated to version 3.11.1, therefore '--careful' option is now enabled by default (Linux version only).
  • NEW: Samples can be moved to another project in batch mode (available in sample search dialog and in File menu).
  • NEW: Samples from database can be used now as input source for pipelines, which allows to reprocess tasks or process new tasks more efficiently for a large number of samples.
  • NEW: Pipeline option to overwrite all existing task entries was added.
  • NEW: Estimated finish time is now shown in pipeline report of running pipelines.
  • NEW: Epidemiological metadata and Tags can be now exported to SPEC files and stored in different project folders (available in menu File | Export Sample Contigs).
  • NEW: Export Sample Contigs allows now to export ACE/BAM instead of FASTA files and FASTQ-file-links to SPEC files.
  • NEW: Sample search result table contains now in right-click menu the new options to copy sample names and create bookmarks.
  • NEW: If during MLST typing no ST could be determined a MLST allele/ST submission info and link to curator website to submit new data is shown in the MLST result window.
  • NEW: Option to initiate a MLST retyping for samples without ST after new alleles/STs have been downloaded was added.
  • CHANGED: An issue with online MLST scheme updates for species with multiple schemes (e.g., Acinetobacter) was fixed.
  • CHANGED: In the SRA download window the option to close the SeqSphere+ main window during download can now be disabled.
  • CHANGED: If a Task Template is used in a project, the ref-seqs. of the targets are not editable any more.
  • NEW: Disk size overview in server administration panel was added.
  • NEW: Pre-defined species-specific database schemes for S. enterica, E. coli, C. difficile, A. baumannii, and N. meningitidis were implemented.
  • CHANGED: An issue with the calculation of expected backup temporary size was fixed.
  • CHANGED: Picard (samtools) was updated to version 2.17.6 to fix a problem with the import of some BAM files.
  • CHANGED: vm was updated to version 8u152.
  • Some GUI revisions, smaller improvements, and bug fixes.

Version 4.1.8/9 (16-Oct-2017)

  • CHANGED: Changed https URL for online NCBI BLAST queries.
  • CHANGED: Fixed assembling/mapping recommendations for some downloaded cgMLST schemes.

Version 4.1.7 (04-Oct-2017)

  • CHANGED: Fixed issue with calculation of expected backup temporary size.

Version 4.1.6 (08-Sep-2017)

  • CHANGED: Fixed issue with initial setting of memory usage in client.

Version 4.1.5 (04-Sep-2017)

  • CHANGED: Fixed SPAdes problem whith blanks in FASTQ filenames (e.g., when downloaded from SRA).

Version 4.1.3/4 (30-Aug-2017)

  • CHANGED: Fixed problem when opening samples to workspace.
  • CHANGED: Sample QC Statistics: Analysis per target is disabled by default (time consuming).

Version 4.1.2 (25-Aug-2017)

  • CHANGED: Fixed check for backup warning if last backup is too old.
  • CHANGED: Handle reads without sequence data in FASTQ files.
  • CHANGED: Added additional size checks (e.g., workspace, comparison table and xls export).

Version 4.1.1 (17-Aug-2017)

  • CHANGED: Fixed allele submission issue for some local allele task templates.

Version 4.1.0 (10-Aug-2017)

  • CHANGED: Make backups only if a sample was saved to database since last backup.
  • CHANGED: Keep backup files increased to 2 if enough disk space is available.
  • CHANGED: Default for the option 'show warning if oldest sample save without backup is older than' was increased from 3 to 7 days.
  • CHANGED: Show warning after login if only 1 backup file is kept and automatic backups are configured.
  • NEW: Enhanced (filtering for duplicates) and improved SRA download function.
  • NEW: Download function for NCBI Genomes to files in Tools menu (e.g., for processing with pipeline).
  • NEW: Option to exclude targets manually from cgMLST target definer.
  • NEW: Support export of concatenated SNVs from result table of 'Find SNVs in Distance Columns' table. Requires that the SNVs columns are shown in the table.
  • NEW: Improved support for two MLST schemes in a project (e.g., for A. baumanii).
  • NEW: Option to hide last used login name in login form. See menu Options | Preferences.
  • CHANGED: Cluster alerts in pipelines are now disabled by default. Can be enabled in the advanced general settings of the script.
  • CHANGED: Renamed field 'Ridom ID' into 'cgMLST.org ID'.
  • CHANGED: Comparison table snapshots limited to 1,000 samples (counting also excluded samples).
  • CHANGED: Fixed parsing issue with incomplete replicons in current NCBI genomes index file.
  • CHANGED: Export Assembly Contigs function now uses newest contigs if multiple procedures exist.
  • CHANGED: File export (e.g., FASTA contigs) no preserves '.' and blank characters in file names.
  • CHANGED: Fixed JVM crashes on Linux that appear after installation of kernel patch for CVE-2017 1000364.
  • CHANGED: Fixed a scaling problem in download progress bar.
  • Some GUI revisions, option renamings, smaller improvements and bugfixes.

Version 4.0.2 (10-May-2017)

  • CHANGED: Fixed a problem with stored metadata export definitions.

Version 4.0.1 (03-May-2017)

  • CHANGED: Added support for PROKKA GenBank files without gene annotations in cgMLST target definer.
  • CHANGED: Fixed a problem with choosing predefined procedure details in pipeline script editor.
  • CHANGED: Fixed a problem with exclusion list of files in pipeline script editor.
  • CHANGED: Default color grouping in comparison table checks for existing values.

Version 4.0.0 (19-Apr-2017)

  • NEW: Possibility to save Comparison Table and minimum spanning tree content as 'Snapshot' (requires server update; menu function and button).
  • NEW: Final and improved release of search for group specific SNV in Comparison Table distance columns (menu function and button).
  • CHANGED: Final and improved release of search for SNV in Comparison Table distance columns (menu function and button).
  • CHANGED: Support in NCBI Genome Browser for new NCBI genomes index file format (includes field 'strain' now).
  • CHANGED: Velvet consensus caller procedure for ambiguity calling changed to obtain more reproducible results. This change might result in a slightly higher number of failed targets but allele numbers still called the same for the remaining targets.
  • CHANGED: Revised configuration of procedure details in pipeline input source and some other minor revisions and renamings in pipeline script.
  • CHANGED: Default coloring of Comparison Table entries changed from cgMLST CT to MLST ST or Epi Info if content available.
  • NEW: Added new field 'Cluster/Outbreak' to default database scheme that is by default shown in Comparison Table.
  • NEW: Added 'Delete Samples' button in toolbar of 'Search Samples' in database result table and minor revision of the toolbar.
  • NEW: Added 'Set Values and Store to Database' function in Comparison table: use this function from the right-click menu when you have selected Sample(s) in the Comparison Table to directly enter and store values for a specific database field.
  • NEW: Added 'Add Additional Samples to Table' menu function and button in Comparison Table: use this function to load additional Samples from the database in your Comparison Table.
  • CHANGED: Improved metadata column choosing option when exporting a xls/csv file from a Comparison Table.
  • CHANGED: Changed parameter unit for keeping old backup files from 'days' to 'number of backup files'. New default value is 1 backup file (requires server update). Therefore, for most users the number of kept backups does not change.
  • NEW: Added option to define zip compression level for backups, new default is 'best speed' that result in 100% speed improvement with only about 10% larger files (requires server update).
  • CHANGED: Added option to use Sample alias ID as name when exporting assembly contigs.
  • CHANGED: SRA FASTQ download now stores available epi metadata together with procedure details in SPEC files.
  • NEW: Import of epi metadata from SPEC files.
  • NEW: Added option in Sample overview procedure tab to 'Add Alternative Path for Local Computer' for sequence data files (ACE/BAM/FASTQ). This allows to access sequences files that are stored on a network device that might be accessible from different computers with different paths.
  • NEW: Added 'distance to reference' plot to coverage optimizer results (not yet public documented) in Sample QC statistic.
  • NEW: Added category field to Projects.
  • CHANGED: Updated to a newer version of biojava library that is required for some GenBank (GB) files.
  • CHANGED: Added function to force deleting user-defined database scheme fields even if field entries exist in (some) Samples (Administrator only). If deleted the field is not only no longer part of a database scheme but the field entries are also deleted in all database Samples.
  • Some GUI revisions, function renamings, smaller improvements and bugfixes.

Version 3.5.3 (30-Jan-2017)

  • CHANGED: Updated fastq-dump software of SRA toolkit to version 2.8.1-2.

Version 3.5.2 (19-Jan-2017)

  • CHANGED: Fixed export function in Unique SNV result for missing non-target genome sequences.

Version 3.5.1 (29-Dec-2016)

  • CHANGED (Linux version only): Adjust executable flag for updated external files in Linux version.

Version 3.5.0 (28-Dec-2016)

  • CHANGED: Support for new NCBI URL in SRA download.
  • CHANGED: Fixed an issue with ENA submission (NCBI Taxonomy ID).
  • CHANGED: Proper handling of missing value terms ('not collected', 'not provided', and 'restricted access') in epi curve and geographical map.
  • CHANGED: SPAdes updated to version 3.9.0 (Linux version only).
  • CHANGED: Removed SPAdes --careful option from default parameter (for new pipelines).
  • CHANGED: Added SPAdes options for thread count, memory usage settings and additional parameters.
  • CHANGED: Discontinued support for Velvet on Linux due to issues with low quality Illumina reads.
  • NEW: Added button to externalize legend window in minimum spanning tree.
  • NEW: Sample bookmarks now support export, import, and direct creation of comparison tables.
  • NEW: Added drop down buttons to shortcuts on welcome page.
  • CHANGED: Added automatic retry on connection errors to NCBI SRA download.
  • CHANGED: Improved Import/Export of color groups in comparison table.
  • CHANGED: Fixed error in comparison table function in search result dialog.
  • CHANGED: In comparison table dialog, no genotyping results are pre-selected if multiple cgMLST schemes exist in a Project.
  • CHANGED: Using file-locks for temporary directory to prevent conflicts of parallel pipelines.
  • CHANGED: Fixed error in enable state of 'Move Samples' function.
  • NEW: Download and install software update for clients by command line parameter (Linux version).
  • CHANGED: Term 'Queries' is replaced by 'Genotypings'.
  • CHANGED: Fixed spelling of 'restricted access'.
  • Some GUI revisions, smaller improvements and bugfixes.

Version 3.4.0 (21-Oct-2016)

  • CHANGED: Revised sample submission anonymization settings and dialogs.
  • CHANGED: Revised Procedure tab in Sample Overview.
  • CHANGED: Changed NCBI access from http to https.
  • CHANGED: Renamed 'Query Libraries' into 'Genotyping Libraries'.
  • CHANGED: Renamed 'WGS Parameters' tab into 'Task Procedure'.
  • CHANGED: Renamed Sequence Specifications into Procedure Specifications.
  • CHANGED: Renamed QC Analysis into Target QC Procedure.
  • CHANGED: Revised HTML export of Graphical Map.
  • CHANGED: Fixed problems with missing FASTQ files in ENA submission.
  • CHANGED: Improved performance of access control checks in large databases.
  • CHANGED: Value 'unknown' for date and country field was replaced by 'not collected' for new entries.
  • CHANGED: Fixed a problem when downloading NCBI draft genomes with thousands of contigs.
  • NEW: Added option to use allele type numbers when creating a Task Template from allelic libraries.
  • NEW: Support SPAdes assembler in pipelines on Linux clients.
  • NEW: Backup settings option to disable size checks on network drives.
  • NEW: Project comparison table, right-click context menu: 'Clear Fields in Selected Samples'.
  • NEW: Filter option in projects, database schemas, and users managing dialogs.
  • Several GUI revisions, smaller improvements and bugfixes.

Version 3.3.0 (02-Aug-2016)

  • NEW: 'Open Comparison Table' button in sample search panel.
  • NEW: Menu function 'Logout & Start Pipeline Mode'.
  • NEW: 'Exclude Files in Pipeline (right-click on file preview).
  • CHANGED: Fixed problems with RAST GenBank files and multiple contigs.
  • CHANGED: When importing downloaded GB files the strain is used as sample ID.
  • CHANGED: Copying of FASTQs in pipeline does not overwrite original files.
  • CHANGED: Improved handling of FASTA files without file extension.
  • NEW: Shortcut button in Comparison Table toolbar to export distance matriy.
  • NEW: Password expiration policy can be defined (requires server update).
  • Several GUI revisions, smaller improvements and bugfixes.

Version 3.2.1 (28-Apr-2016)

  • CHANGED: Fixed a color problem in Geographical Maps.

Version 3.2.0 (27-Apr-2016)

  • NEW: Support for organisms with non-default codon translation tables (e.g., Mycoplasma).
  • NEW: Export phylogenetic and minimum spanning tree to EMF+ file.
  • NEW: Define backup temp directory in backup settings (requires server update).
  • NEW: Added 'Exit and Restart' button to pipeline mode.
  • NEW: Comparison table tooltips: Showing Sample ID and reasons for missing data.
  • NEW: Show grouped-by and citation hints in exported trees.
  • NEW: Download from NCBI directly into FASTA files.
  • NEW: Unique SNVs finder (beta).
  • NEW: Beta-Support SPAdes assembler in pipeline on Linux (beta).
  • CHANGED: Revised 'Files' tab and renamed to 'Procedure' in Sample overview panel.
  • CHANGED: Revised field data import.
  • CHANGED: Update files require certificate.
  • CHANGED: Removed internal readid in fastq files downloaded from SRA.
  • CHANGED: NCBI download of master records with single contig was fixed.
  • Several GUI revisions, smaller improvements and bugfixes.

Version 3.1.0 (21-Jan-2016)

  • NEW: Support multiple chromosomes and scaffolds/contigs as reference genome in cgMLST target definer.
  • NEW: Export phylogenetic and minimum spanning tree to EMF file.
  • CHANGED: Revised SRA download with support of HTTP proxy.
  • CHANGED: ENA Submission authentication changed.
  • NEW: Copy phylogenetic and minimum spanning tree to clipboard.
  • NEW: Added field 'Lat/Long Resolution' to default database schema (requires server update).
  • NEW: Added pipeline option to allow exporting contigs to fasta files.
  • NEW: Pipeline file naming specifications of sequence files can be defined on full paths.
  • NEW: Background in home panel.
  • NEW: Export core and/or accessory genome gene concatenated SNPs as FASTA.
  • NEW: User role provilege 'Edit existing projects' to define user accounts that may not create new projects but edit existing ones (requires server update).
  • CHANGED: Support for various codon translation tables.
  • CHANGED: Optionally export comparison table without distance columns.
  • CHANGED: Option to keep all reads in Task Template.
  • CHANGED: Export legend of phylogenetic and minimum spanning tree in separate file.
  • CHANGED: Fixed a downsampling issue in BWA processing.
  • NEW: See Help | Citations for citing correctly in publications the used tools.
  • CHANGED: Reduced size of temporary files during pipeline processing.
  • Several GUI revisions, smaller improvements and bugfixes.

Version 3.0.1 (09-Sep-2015)

  • CHANGED: Fixed naming of Samples in MST complexes.
  • CHANGED: Handling of decimal numbers in average coverage of NCBI Genomes.

Version 3.0.0 (07-Sep-2015)

  • NEW: Draw Geographical Map for Samples from a comparison table.
  • NEW: Draw Epi Curve for Samples from a comparison table.
  • NEW: Create Sample report in Result tab of a Sample.
  • NEW: Download FASTQ files from NCBI SRA.
  • CHANGED: Renamed MLST+ to cgMLST.
  • NEW: Assign tags in sample search dialog.
  • CHANGED: Renamed "missing targets" to "not found targets".
  • CHANGED: Revised NCBI Genome Browser.
  • CHANGED: Revised tag assigning dialogs.
  • CHANGED: Revised backup process.
  • CHANGED: Added sample ID to contig names when exporting assembly contigs.
  • CHANGED: Allow submission of new alleles without place and time information.
  • CHANGED: Revised paths in filestorage structure.
  • NEW: Move samples between projects (requires administrator rights).
  • Several GUI revisions, smaller improvements and bugfixes.

Version 2.4.0 (08-Jun-2015)

  • NEW: Stop/Cancel running pipelines from other clients.
  • CHANGED: NCBI Genome Browser was revised with current NCBI categories and is up-to-date with NCBI website now.
  • CHANGED: Project dialog (menu Options|Projects) now allows to delete whole projects with samples.
  • NEW: Last comparison table shortcut in home panel.
  • NEW: Support of regular expression for file name matching in pipeline.
  • NEW: Option to ignore illegal reads in BAM file.
  • CHANGED: Revised antimicrobial fields and added import functionality (requires server update).
  • CHANGED: Target sequence export dialog was improved with orientation and sequence naming.
  • CHANGED: Pipeline default for file storage of Assembled/Mapped files is now 'Link to files'.
  • CHANGED: MLST schemes are scanning for all alleles now to find highly varying alleles.
  • CHANGED: Fixed X11 forwarding for server.
  • CHANGED: Switched port for ENA ftp submission of reads.
  • CHANGED: Handling changed profile definition of some MLST schemes (e.g., A. baumanii).
  • Several GUI revisions, smaller improvements and bugfixes.

Version 2.3.1 (08-Apr-2015)

  • CHANGED: Introduced MLST+ Target Definer version, now version 1.1.
  • CHANGED: Allow using contigs only for reprocessing if assembly files are not available.
  • CHANGED: Exporting distance matrix to xlsx.
  • NEW: Adding sequence specification fields to existing Comparison Table.
  • CHANGED: Fixed a problem with distance line styles in MST.
  • CHANGED: Fixed problems for changed PubMLST loci names.
  • CHANGED: Sequence Statistics are now calculated for FASTA files too.
  • CHANGED: Comparison table groups default by Cluster Type if existing.
  • NEW: Export/Import Sequence Specifications.
  • CHANGED: Allow to disable proxy for SeqSphere+ server.

Version 2.3.0 (20-Jan-2015)

  • NEW: Automatically update MLST profiles from Internet.
  • NEW: Results tab in Sample overview shows a summary of the important result fields.
  • NEW: Scanning details in Files tab shows a description of the used paramters.
  • CHANGED: Improved submission of read data to ENA SRA.
  • CHANGED: Improved administration of raw read, assembly, and contig assembly data.
  • CHANGED: Substitution rate is warning by default.
  • CHANGED: Automatic Homopolymer correction can only be enabled if data is specified as for IonTorrent or 454.
  • CHANGED: Improved speed of backups.
  • CHANGED: Fixed version problem in Windows service installer.
  • Several GUI revisions, smaller improvements and bugfixes.

Version 2.2.1 (26-Nov-2014)

  • CHANGED: Fixed a problem with some FASTQ files.
  • CHANGED: Fixed a problem with some proxy servers.

Version 2.2.0 (31-Oct-2014)

  • NEW: Storage and submission of assembly contigs.
  • NEW: Submission of read data to ENA SRA.
  • NEW: Cluster-alerts and revised pipeline report.
  • CHANGED: Batch mode is now default for import of genome data.
  • CHANGED: Fixed a problem in database scheme editor.
  • CHANGED: Support for older Linux versions.
  • CHANGED: Revised tag selection dialogs.
  • Several GUI revisions, smaller improvements and bugfixes.

Version 2.1.4 (23-Sep-2014)

  • CHANGED: Replaced BLAST library in 32-bit Windows version.

Version 2.1.3 (03-Sep-2014)

  • CHANGED: Changed handling of uncovered regions in BAM files.

Version 2.1.2 (02-Sep-2014)

  • CHANGED: Fixed memory problem in BLAST integration.

Version 2.1.1 (28-Aug-2014)

  • CHANGED: Compression of file uploaded to Server.

Version 2.1.0 (28-July-2014)

  • CHANGED: Target analysis checks can be defined as warnings only. Therefore colors of state icon (e.g., smiley) where changed.
  • CHANGED: Default setting of coverage check for new Task Templates Target and for published Task Templates was changed (Old: Error if min. coverage is below 10; New: Warning if min. coverage is below 5).
  • CHANGED: Submission to nomenclature server of sequence data without read alignment (e.g., FASTA files) is allowed.
  • CHANGED: Coverage analysis check can be changed and disabled for global Task Templates downloaded from store.
  • CHANGED: Removed field Collector email from Sample submission dialog.
  • NEW: Use 'Reprocess Samples' to start a batch job for existing Samples (see Tools menu).
  • NEW: In sample submission field values can be copied to other samples.
  • NEW: Define 'unknown' in anonymization filter for Sample submission.
  • NEW: Linux 64bit version of client available.
  • NEW: Find nucleotide variants between the targets of two or more samples.
  • NEW: Download read data from ENA SRA.
  • NEW: Update function for downloaded published Task Templates.
  • NEW: Home panel shows recent pipeline reports.
  • CHANGED: Default access rights for new Projects and Task Templates was set to 'anyone'.
  • CHANGED: Genome scan or allele libraries prefers hits with unique 100% matches.
  • CHANGED: Pipeline waits while database backup performs.
  • CHANGED: Pipeline allows multiple logins with same user account (useful for scaling).
  • CHANGED: Fixed problems with xBASE and RAST GenBank files.
  • CHANGED: Velvet assembler integration uses consensus caller for consensus error correction.
  • CHANGED: Changed visible default columns in target table of Task Template.
  • Several GUI revisions, smaller improvements and bugfixes.

Version 2.0.1 (14-May-2014)

  • CHANGED: Server only: Removes temporary files when creating backups.

Version 2.0.0 (09-May-2014)

  • NEW: Define and start a pipeline to assemble, import, type and analyze hundreds of your WGS sequence data at once automatically.
  • NEW: Velvet Assembler: Run WGS assembly with an integrated Velvet and automatic kmer optimization (Windows 64bit version).
  • NEW: BWA Mapper: Run WGS mapping against a reference genome or multiple reference sequences (Windows 64bit version).
  • NEW: Browse NCBI: Browse, filter and download genomes that are available at the NCBI GenBank ftp site.
  • NEW: File Storage: Store the original WGS data files (e.g., ace or bam) on the server linked to the Sample entry.
  • NEW: Mixed Task Templates: Create Task Templates that can handle WGS and Sanger sequence data with different analysis settings.
  • NEW: Exclude in MLST+ Target Definer genes that were found in selected plasmids.
  • CHANGED: Use mapping quality in SAM/BAM import.
  • CHANGED: Collected-by was set to not mandatory fo Sample Submission.
  • Several GUI revisions, smaller improvements and bugfixes.

Version 1.0.1 (15-Dec-2013)

  • NEW: Multithread support for integrated blast in Windows 64bit version.
  • NEW: Multithread support for distance calculation in trees.
  • CHANGED: Improved nomenclature server submission process.
  • CHANGED: Improved MST and phylogenetic trees.
  • NEW: Comparison Table: Added statistic functions.
  • NEW: Comparison Table: Added function to add further columns.
  • NEW: Comparison Table: Added recreate function in file menu.
  • NEW: Compariosn Table: Changed managing dialog.
  • CHANGED: Minor changes in user management dialog.
  • Several GUI revisions, smaller improvements and bugfixes.

Version 1.0.0 (18-Nov-2013)

  • First release of SeqSphere+.

Version 0.99 (April-2013)