Center for Genomic Epidemiology

Due to planned maintenance the services will be down on the 15th and 16th of August 2022. We are sorry for any inconvenience.

Overview of Services

Phenotyping
  • ResFinder
    Identifcation of acquired antibiotic resistance genes.
  • ResFinderFG
    Identifcation of functional metagenomic antibiotic resistance determinants.
  • LRE-finder
    Identifcation of genes and mutations leading to linezolid resistance.
  • KmerResistance
    Identifcation of acquired antibiotic resistance genes using Kmers.
  • PathogenFinder
    Prediction of a bacteria's pathogenicity towards human hosts.
  • VirulenceFinder
    Identifcation of acquired virulence genes.
  • Restriction-ModificationFinder
    Determination of Restriction-Modification sites (based on REBASE.)
  • SPIFinder
    SPIFinder identifies Salmonella Pathogenicity Islands.
  • ToxFinder
    ToxFinder identifies genes involved in mycotoxin synthesis.
Typing
  • MLST
    Multi Locus Sequence Typing (MLST) from an assembled genome or from a set of reads.
  • PlasmidFinder
    PlasmidFinder identifies plasmids in total or partial sequenced isolates of bacteria.
  • pMLST
    Multi Locus Sequence Typing (MLST) from an assembled plasmid or from a set of reads.
  • cgMLSTFinder
    Core genome Multi Locus Sequence Typing (cgMLST) from a set of reads.
  • KmerFinder
    Prediction of bacterial species using a fast K-mer algorithm.
  • MGE
    Identification of mobile genetic elements and their relation to antimicrobial resistance genes and virulence factors.
  • SpeciesFinder
    Prediction of bacterial species using the S16 ribosomal DNA sequence.
  • SeroTypeFinder
    Prediction of serotypes in total or partial sequenced isolates of E. coli.
  • SeqSero
    SeqSero predicts the Salmonella serotype of either the pre-assembled or raw read sequence data provided to the service.
  • spaTyper
    spaTyper predicts the S. aureus spa type.
  • FimTyper
    FimTyper predicts the E. coli Fim type.
  • CHTyper
    CHTyper predicts the E. coli FimH type and FumC type.
  • PAst
    PAst predicts the P. aeruginosa serotypes.
  • SCCmecFinder
    SCCmecFinder identifies SCCmec elements in sequenced S. aureus isolate.
Phylogeny
  • MINTyper
    Identification of SNPs with automatic filtering, masking and site validation together with inferred phylogeny based on both long and short sequencing data.
  • CSIPhylogeny
    CSI Phylogeny calls SNPs, filters the SNPs, does site validation and infers a phylogeny based on the concatenated alignment of the high quality* SNPs.
  • NDtree
    NDtree constructs phylogenetic trees from Single-End or Pair-End FASTQ files.
  • Evergreen
    Evergreen generates a forest of constantly updated phylogenetic trees with publicly available whole-genome sequencing data from foodborne, bacterial isolates that were deposited in the short sequencing read archives (NCBI SRA/ENA).
  • TreeViewer
    Phylogeny Tree Viewer.
Metagenomics
  • CCMetagen
    CCMetagen: Comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data.
PCR-tools
  • RUCS
    RUCS: Rapid Identification of PCR Primers Pairs for Unique Core Sequences.
Other
  • MyKMAfinder
    MyKMAfinder performs typing or pheno typing using KMA based on a user defined database.
  • MyDbFinder
    MyDbFinder performs typing or pheno typing using blast based on a user defined database.
  • MyKmerFinder
    MyKmerFinder performs typing or pheno typing using Kmers based on a user defined database.
  • DeHumanizer
    The DeHumanizer web-server is a tool for human filtering based on the method described by Zhang et al.
  • HostPhinder
    HostPhinder identifies the bacterial host of a query phage genome based on its genomic similarity to a database of phage genomes with known host.
  • MetaPhinder
    MetaPhinder: Identifying Bacteriophage Sequences in Metagenomic Data Sets.