Overview of Services
Phenotyping
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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
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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
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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
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CCMetagen
CCMetagen: Comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data.
PCR-tools
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RUCS
RUCS: Rapid Identification of PCR Primers Pairs for Unique Core Sequences.
Other
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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.