Ridom SeqSphere+ version 8.0
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).
- 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).