Ridom SeqSphere+ version 8.0

Major Changes

  • 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.
  • Opening Comparison Tables with thousands of samples has been accelerated by a factor of about 20x.
  • 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).
  • New numeric sorting of number only columns in Comparison Table for correct sorting of those columns (previously alpha-numeric).
  • Sample tags can now be searched with boolean expressions in the advanced mode of the search.
  • Setting of genus and species database fields of Sample automatically according to Mash result (previously taken statically from the cgMLST Task Template).
  • Updated SKESA assembler to version 2.4 (produces identical results as previous version).
  • SARS-CoV-2 pangolin task template and server updated to handle and show Scorpio results (including WHO label).