Center for Genomic Epidemiology

Overview of Services

Announcements

  • May 01 - 2025

    New CGE tools platform. We are pleased to announce our new online tools platform. Please update your bookmarks.

    This page is now considered a legacy page and will no longer be maintained. We will continue to move popular services to our new platform over the coming months. Once that process is complete, we will take this page offline. Please do not hesitate to contact us, if you have any questions.
    -- The CGE tools development team.

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
     The HostPhinder tool is no longer being supported.
  • MetaPhinder
     MetaPhinder: Identifying Bacteriophage Sequences in Metagenomic Data Sets.
Command line Tools
  • Flankophile
     Flankophile is a pipeline build for easy analysis and visualization of gene synteny