The COllaborative Management Platform for detection and Analyses of (Re-) emerging and foodborne outbreaks in Europe is a collaboration of 29 institutions with experience in outbreak detection and response in areas of human health, animal health and food safety. COMPARE is a large EU project with the intention to speed up the detection of and response to disease outbreaks among humans and animals worldwide through the use of new genome technology. The aim is to reduce the impact and cost of disease outbreaks.

More information about COMPARE can be found at:

COMPARE Reference Genomes

This COMPARE Reference Genomes page offers a curated selection of published reference sequences covering viral (Norovirus, Hepatitis A virus), bacterial (Salmonella enterica enterica, Listeria monocytogenes, Escherichia coli) and protozoan (Cryptosporidium) genomes. The set of reference genomes has been selected to cover some of the most important foodborne pathogens, which are of great public health relevance. The reference genome set is provided as a first step in enabling standardized, comparable genomic analysis within each of the organisms. For each of the organisms the reference set has been selected to cover the most important clusters/types, to the extent possible with the publically available genomes.

These sets of reference sequences can be used to reliably and exhaustively for local alignment searches, to map/annotate or genotype NGS reads or contigs originating from the corresponding microorganisms, from any type of NGS experiment. The sets are periodically updated, and new sets for additional microorganisms are added, as soon as new data become available through the COMPARE project.

These reference sets are used by the following COMPARE NGS analysis tools/pipelines.

More information by microorganism:

Hepatitis A virus
Salmonella enterica
Listeria monocytogenes
Escherichia coli

Data retrieval

To retrieve the complete COMPARE Reference Genomes dataset in the browser please go here:
and select 'COMPARE-RefGenome' as the XREF source. Please use the 'expanded' option to see the complete taxonomic information.

Programmatic retrieval of the complete COMPARE Reference Genomes dataset can be done via the following URL:

ENA sequence or sample accessions for a single sample/isolate in the dataset can be returned using the following URL:<source>&source_accession=<source_accession>
where source_accession is the isolate/sample name as shown in the table below, for example:

The ENA record, shown in the 'Target primary accession' column of the result from the above URL, can be retrieved with the following URL:<Target_primary_accession>
where Target_primary_accession has been inserted from the response to the previous URL (e.g.

More extensive functions are described for REST services relating to the COMPARE Reference Genomes. Users should note that records in the dataset are served from ENA and are denoted as belonging to the dataset through ENA cross-reference annotations.

Latest ENA news

11 Oct 2017: Read data download issues resolved

Read data download issues previously affecting and services now resolved.

06 Oct 2017: ENA read data download issues

Issues with read data download from and

04 Oct 2017: ENA Release 133

Release 133 of ENA's assembled/annotated sequences now available