Biorepositories and Databases

Biorepositories and Databases

This page contains documents and links related to biorepositories that provide reference materials, and databases of importance for molecular analysis of pathogens included in the EURGen-RefLabCap project.

 

Culture Collections

 

American Type Culture Collection (ATCC): The Global Bioresource Center

National Collection of Type Cultures (NCTC)

German Collection of Microorganisms and Cell Cultures (DSMZ)

Bioinformatics tools relevant for CCRE analyses

Tool

Purpose

Tool

Purpose

KmerFinder

Taxonomy

VirulenceFinder

VF detection

Speciator

Taxonomy

VFanalyzer

VF detection

SerotypeFinder

Serotyping

Victors

VF detection

MLST

Phylogeny

PlasmidFinder

Plasmid ID

rMLST

Taxonomy, phylogeny

COPLA

Plasmid ID

cgMLST

Phylogeny

PlasmidSeeker

Plasmid ID

CSIPhylogeny

Phylogeny

Platon

Plasmid ID

NDTree

Phylogeny

MOB-suite

Plasmid typing

Evergreen

Phylogeny

pMLST

Plasmid typing

FastTree

Phylogeny

MobileElementFinder

Mobile elements detection

SRST2

AMR detection, phylogeny

MGEFinder

Mobile elements detection

ARIBA

AMR detection, phylogeny

Kleborate

Multiple genomic analyses

KmerResistance

Taxonomy, AMR detection

Pathogenwatch

Multiple genomic analyses

ResFinder

AMR detection

Enterobase

Multiple genomic analyses

PointFinder

AMR detection

BIGSdb

Multiple genomic analyses

RGI

AMR detection

NCBI Pathogen Detection

Multiple genomic analyses

AMRFinder

AMR detection

IRIDA

Multiple genomic analyses

SSTAR

AMR detection

ARIES

Multiple genomic analyses

ABRicate

AMR detection

PATRIC

Multiple genomic analyses

CARD

AMR detection

Ridom SeqSphere+

Multiple genomic analyses

 

Public databases relevant for CCRE analyses

Database

Purpose

Database

Purpose

NCBI

Collection and curation of all nucleotide sequences

MBLED

AMR detection

ENA

Collection and curation of all nucleotide sequences

u-CARE

AMR detection

SILVA

Taxonomy

BacMet

Gene detection

GreenGenes

Taxonomy

PHI-BASE

VF detection

NDARO

AMR detection

PLSDB

Plasmid detection

ARG-ANNOT

AMR detection

COMPASS

Plasmid detection

MEGARes

Gene detection

ISFinder

IS detection

ABRES Finder

AMR detection

Integrall

Integron detection

BLDB

AMR detection

ICEberg

Integron detection

CBMAR

AMR detection

The Transposon Registry

Transposon detection

LacED

AMR detection

 

 

https://www.eurgen-reflabcap.eu/resources/biorepositories-and-databases
14 DECEMBER 2024