Expasy: Swiss Bioinformatics Resource Portal
e.g. BLAST, UniProt, MSH6, Albumin...

SPSP | Swiss Pathogen Surveillance Platform

  • Genes & Genomes
  • Database
  • Software tool
The Swiss Pathogen Surveillance Platform (SPSP) is a secure One-health online platform that enables near real-time sharing under controlled access of pathogen whole genome sequences and their associated sensitive clinical/epidemiological metadata. The submitted raw next-generation sequencing (NGS) data are analyzed using harmonized bioinformatics methods for quality control, assembly, typing, resistance/virulence, and outbreak analyses.

This resource supports COVID-19 / SARS-CoV-2 research.
Browse the resource website

Developed by the Clinical Bioinformatics group, in collaboration with the University Hospitals of Basel, Geneva, Lausanne; VetSuisse Bern and Zurich; and the Universities of Basel, Bern and Zurich.

You might also be interested in

      • Genes & Genomes
      • Proteins & Proteomes
      • Structural Biology
      • Database

    ViralZone

    Fact sheets about viruses linked to sequence databases
      • Glycomics
      • Database

    SugarBind

    Pathogen Sugar-Binding Database
      • Genomics
      • Population genetics
      • Software tool

    V-pipe

    Viral genomics pipeline
      • Genomics
      • Population genetics
      • Software tool

    V-pipe SARS-CoV-2

    V-pipe pipeline for SARS-CoV-2 sequencing data
      • Text mining & Machine learning
      • Software tool

    COVTriage

    Rank the COVID-19 literature according to COVoc ontology
      • Genomics
      • Evolution & Phylogeny
      • Software tool

    Nextclade

    Clade assignment, mutation calling & QC for virus sequences
      • Genes & Genomes
      • Evolution biology
      • Software tool

    BEAST2

    Bayesian evolutionary analysis by sampling trees
      • Genes & Genomes
      • Evolution biology
      • Software tool

    GenSpectrum

    Real-time pathogen genomic sequence analysis
      • Evolution & Phylogeny
      • Database

    OrthoDB

    Ortholog evolutionary and functional annotations
      • Proteins & Proteomes
      • Glycomics
      • Database
      • Software tool

    GlyConnect

    Integrated data platform to study glycosylation
      • Genomics
      • Evolution biology
      • Software tool

    Nextstrain

    Impact of pathogen genome data on science and public health
      • Genomics
      • , Transcriptomics
      • Evolution biology
      • Software tool

    BUSCO

    From QC to gene prediction and phylogenomics
      • Evolution & Phylogeny
      • Software tool

    OrthoLoger

    Accurate and scalable inference of groups of orthologs
      • Proteins & Proteomes
      • Database
      • Software tool

    HAMAP

    UniProtKB family classification and annotation
      • Genomics
      • Database

    TASmania

    Toxin-antitoxin database
      • Genomics
      • Software tool

    TASer

    Search tool associated to TASmania