MAY 2022
EPISEQ® CS v1.2.0
WHAT'S CHANGED?
-
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
-
OCTOBER 2020
EPISEQ® CS v1.1.0
WHAT'S CHANGED?
-
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
WHAT'S CHANGED?
-
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
-
DECEMBER 2019
EPISEQ® CS v1.0.2
WHAT'S CHANGED?
-
User interface:
-
Multiple minor fixes and improvements
-
Improved display of virulome and resistome results
-
-
Online help:
-
Updated topics
-
OCTOBER 2019
EPISEQ® CS v1.0.1
WHAT'S CHANGED?
-
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
-