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MAY 2022
EPISEQ® CS v1.2.0


  • Sequence analysis pipeline:

    • List of bacterial species has been extended with Citrobacter freundii

    • Integrated plasmid functionality to detect plasmid contigs in the genome

    • Serotyping and pathotyping performed on samples identified as Escherichia coli / Shigella

    • MLST and Spa typing databases: allele nomenclature refreshed

    • Resistome database: growing content while further improving the curation* (details in the updated online help)

    • Virulome database: growing content and screening now available for most species* (details in the updated online help)

    • Upload and processing of FASTA gzip files

* As the nomenclature of some markers is evolving and this evolution is integrated in the databases, please compare results obtained with different versions of EPISEQ® CS with caution.​ Please note that previously analyzed sample are not reprocessed with the new pipeline and database.

  • General:

    • Google Chrome added as supported browser

    • Internet Explorer removed as supported browser

    • Dashboard on the home page with information about the underlying credit plan, wet lab performance, time analysis of uploads and resistance genes occurrence

    • New button to select all (filtered) samples

    • Download button made more visible in all panels

  • Sample results:

    • Resistome sample window:

      • Filtering lists available for Resistance mechanism categories, Drug and Drug families

      • Extra column displaying the type of mutation

      • Extra column reporting the plasmid accession in case the marker is found on a plasmid contig

    • Virulome sample window:

      • Extra information available for every marker hit (Reference locus, Citation, ecNumber, uniprot, pfam, …)   

      • Extra column reporting the plasmid accession in case the marker is found on a plasmid contig

    • QC sample window:

      • Parameter is displayed that caused a sample to fail

  • Epidemiological analysis:

    • Metadata panel:

      • Color metadata columns based on field content

      • Configuration of the metadata columns is saved in user settings

      • Creation of a panel based on any sample selection

    • Resistome and Virulome panels:

      • Indication when marker is located on a plasmid contig

      • Equivalent hits are excluded from counted hits

      • Mutations at different positions on the same gene, each responsible for a certain resistance, are split over different columns

    • Minimum spanning tree:

      • Samples with distance 0 are grouped inside the same node

      • Node size reflects the number of samples contained in a node

      • Metadata fields can be picked as node identifier

      • New button to stretch/shrink the tree in the available space

  • Bug fixes:

    • Cluster colors displayed on a dendrogram match those in the Report when the cluster cut-off value is changed

    • Calculated MLST column content is displayed if enabled

    • Clearing the collection date of a sample now results in a blank field

    • Branches in a Minimum spanning tree are scaled according to allele differences

    • Resistome data for Pseudomonas aeruginosa is displayed in the Sample resistome window

EPISEQ® CS v1.1.0


  • Database updates:

    • MLST and Spa typing databases: allele nomenclature refreshed

    • Resistome database: growing content while further improving the curation (details provided in the updated online help)

  • Epidemiological analysis window:

    • Minimum spanning tree

    • Filtering of resistome and virulome markers

  • Filtering samples and panels:

    • Filtering of samples based on meta data and typing fields

    • Filtering of panels based on the detected species

  • Sample card:

    • Name(s) of the uploaded file(s) is displayed

    • Pipeline and KB versions are reported

    • Delete button in case of a process/data fail

  • Sample resistome results:

    • Filtering and sorting of resistome markers

    • Additional resistome fields: citation DOI number(s), ARO, uniprot, pfam, …

    • Unknown mutations can be consulted

    • Perfect hits are displayed in green

  • Sample virulome results:

    • Filtering and sorting of virulome markers

    • Perfect hits are displayed in green

  • QC details:

    • Parameters are displayed in the Identity check card

    • Parameters are displayed in the Contamination card

  • Upload grid:

    • New field states are available, including the “Unknown” field for every list

    • Country is default set to “Unknown”

  • User interface:

    • Updated look and feel

    • Uploads tab is removed

  • Performance:

    • Better and faster processing of sample files

  • Online help:

    • New and updated topics

APRIL 2020
EPISEQ® CS v1.0.3


  • Upload grid:

    • Multiple rows can be selected and removed in batch  

  • Epidemiological analysis window: 

    • Better distinction between different cluster colors  

    • Panels are sized according to the available space 

    • Resistome and virulome data are rendered more quickly 

  • Reports: 

    • Cluster colors are transferred to the report 

    • Long samples names are better displayed  

    • Rendering of reports is faster.  

  • Upload card: 

    • All failed samples are summarized in the upload card  

  • Panel card:  

    • Similarities are calculated for user created panels 

  • QC results:  

    • Same QC notations are used throughout the application 

    • Grey QC warning notations are displayed for red failed samples 

  • Resistome results: 

    • Improved pipeline to better handle duplicate hits  

    • Resistome results are sorted alphabetically  

  • Credit management: 

    • Credits are automatically reimbursed when a process fail occurs 

  • Process fail management: 

    • Adjustments are made to reduce the amount of process fails 

  • Online help:  

    • Updated topics 

  • User interface: 

    • Application visual was changed 

EPISEQ® CS v1.0.2


  • User interface:  

    • Multiple minor fixes and improvements  

    • Improved display of virulome and resistome results  

  • Online help:  

    • Updated topics 

EPISEQ® CS v1.0.1


  • Resistome and virulome markers:  

    • Improved handling of resistome and virulome markers 

  • Upload grid:  

    • Added dropdown lists for ‘Host’ and ‘Disease’ fields 

  • Panel card: 

    • Added number of strains in a panel analysis. 

  • Export: 

    • Sheets for resistome and virulome when exporting meta data 

    • Table export button 

  • Online help:  

    • Updated topics 

  • Miscellaneous: 

    • Various smaller bug fixes 

    • Password requirements made more lenient 

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