Databases and public repositories

On this page you will find descriptions and links to databases and data repositories relevant for research on pathogen data. We have selected these resources because they are public and freely available.
The Pathogens Portal
European Nucleotide Archive
Recommended Databases
Tags | Link | Description | Domains | |
---|---|---|---|---|
COVID-19 Data Portal | Covid-19 SARS-CoV-2 | Raw and assembled sequence and analysis of SARS-CoV-2 and other coronaviruses | Bacteria | |
pubMLST | MLST | Public databases for molecular typing and microbial genome diversity including multiple pathogen species | Bacteria | |
BIGSdb-Pasteur | MLST | Web platform with collections of curated databases of bacterial isolates, genomes and genotypes | Bacteria | |
NDARO | AMR | National Database of Antibiotic Resistant Organisms (NDARO), a centralized hub for researchers to access AMR data | Bacteria | |
CARD database | AMR | The Comprehensive Antibiotic Resistance Database (CARD) is a bioinformatic database of resistance genes, their products and associated phenotypes. | Bacteria | |
The Pseudomonas Genome Database | Pseudomonas Genomes | High quality genome annotation of pseudomonas strains, including pathway annotations and AMR Gene Predictions | Bacteria | |
PLSDB | Plasmids | Bacterial plasmids retrieved from the NCBI nucleotide database with additional annotations consist of resistance and virulence factors | Bacteria | |
COVID-19 (SARS-CoV-2 Database) | Covid-19 Genomes | Covid-19 | Virus | |
BV-BRC | Genomes Proteins Experimental data Plasmids Metagenomes | Bacterial and Viral Bioinformatics Resource Center (BV-BRC) encompasses integrated datasets from mainly pathogenic bacteria, archaea, viruses, and eukaryotes | Virus Bacteria Archaea Eukaryote | |
Virus-Host DB | Pathogen-host | Virus-Host DB organizes data about the relationships between viruses and their hosts, represented in the form of pairs of NCBI taxonomy IDs for viruses and their hosts | Virus | |
EuPathDB | Genomes Genes Pathogen-host | The Eukaryotic Pathogen Database (EuPathDB) is an integrated database covering numerous eukaryotic pathogens including Plasmodium and Trypanosoma | Eukaryote | |
PHI-base | Pathogen-host Genes | PHI-base is to provide expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions that are of medical and agronomical importance | Fungi Bacteria |