Center for Genomic Epidemiology

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.