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EuPathDB-Clean is a set of eukaryotic pathogen genomes originally downloaded from the EuPathDB Resource Project established by the National Institute of Allergy and Infectious Disease (NIAID/NIH). These draft genomes were processed to remove all contaminating and low-complexity sequences.

Here we provide the cleaned eukaryotic pathogen genome FASTA files that can be used with any metagenomics classification/analysis programs. For use, download each of the .tgz files and untar the FASTA files using:
  • for file in *.tgz; do tar -xvzf $file -C my_eupathDB_folder/; done

EuPathDB46 vs. EuPathDB26

As of December 1, 2020, we are releasing EuPathDB46-Clean. As compared to EuPathDB-28 (245 genomes), this database is larger (388 genomes) with fewer contaminating sequences. The database underwent the same contamination/low-complexity removal process with updated reference bacterial, archaeal, viral, vertebrate, and plant sequences.

EuPathDB-46 Downloads

EuPathDB-46: Kraken 2 Database
At the link above, we provide the pre-built Kraken 2 database along with the relevant Bracken files. The database is built from ONLY EuPathDB-46 genomes. In order to add EuPathDB-46 to an existing database, users will need to download the genomes themselves and build a new database.

EuPathDB46_Contents.txt lists all genomes in the database, including details about the filename, type, genus, species, and strain.

To build a database containing these genomes:
  1. Make a folder for the database: mkdir my_db
  2. Change directory to the database folder: cd my_db
  3. Download the NCBI taxonomy: kraken2-build --download-taxonomy --db .
  4. Download the file for EuPathDB46: wget
  5. Make a libarary folder: mkdir library
  6. Move to the library folder: cd library/
  7. Download all of the genomes using the links below: wget
  8. Uncompress all of the genome folders: tar -xzvf AmoebaDB46.tgz
  9. Move back to the database folder: cd ../
  10. Build the Kraken/Kraken 2 database: kraken2-build --build --db .

Class Genus Composition * Number of EuPathDB-48 Files Download Uncompressed
AmoebaDB Acanthamoeba, Entamoeba, Naegleria 30 AmoebaDB46_Clean.tgz (360 Mb) 1.39 Gb
CryptoDB Chromera, Cryptosporidium,
Gregarina, Vitrella
18 CryptoDB46_Clean.tgz (98 Mb) 345 Mb
FungiDB Allomyces, Aspergillus, Candida, Clavispora, Coccidioides, Coprinopsis, Histoplasma, Malassezia, Melampsora, Mucor, Penicillium, Pythium, Saccharomyces, Yarrowia, etc. 164 FungiDB46_Clean.tgz (1.8 Gb) 6.2 Gb
GiardiaDB Giardia, Monocercomonoides, Spironucleus 10 GiardiaDB46_Clean.tgz (50 Mb) 179 Mb
MicrosporidiaDB Anncaliia, Edhazardia, Enterospora, Hepatospora, Mitosporidium, Nematocida, Spraguea, Vittaforma, etc. 35 MicrosporidiaDB46_Clean.tgz (62 Mb) 245 Mb
PiroplasmaDB Babesia, Cytauxzoon, Theileria 10 PiroplasmaDB46_Clean.tgz (29 Mb) 101 Mb
PlasmoDB Plasmodium 45 PlasmoDB46_Clean.tgz (185 Mb) 1.1 Gb
ToxoDB Cyclospora, Cystoisospora, Eimeria, Hammondia, Neospora, Sarcocystis, Toxoplasma 33 ToxoDB46_Clean.tgz (550 Mb) 2.1 Gb
TrichDB Trichomonas 1 TrichDB46_Clean.tgz (50 Mb) 180 Mb
TriTrypDB Blechomonas, Bodo, Leishmania, Leptomonas, Paratrypanosoma, Trypanosoma 42 TriTrypDB46_Clean.tgz (406 Mb) 1.5 Gb
Total EuPathDB-46-Clean 388 13.4 GB

EuPathDB-28 Downloads

EuPathDB-28 Library: eupathDB.tar.gz (2.2 GB)
This file contains all 245 genomes in a single folder. Each genome is a multi-fasta file with Kraken and Kraken2-compatible headers. To build a Kraken/Kraken2 database with these files, unzip the folder and place it directly within the library/ folder.
  • For example, to build a database with human, bacteria, and eupathDB:
  • tar -xzvf eupathDB.tar.gz [creates library folder with eupathDB files]
  • mv library/ $DBNAME/library/
  • kraken2-build --download-library bacteria --db $DBNAME
  • kraken2-build --download-library human --db $DBNAME
  • kraken2-build --build --db $DBNAME

  • (It is NOT required to use kraken2-build --add-to-library for these files.)

EuPathDB-28 Kraken2 Database: eupathDB_kraken2.tar.gz (5.6 GB)
This folder is a pre-built Kraken2 database of the 245 eupathDB genomes. It contains three files: hash.k2d, opts.k2d, and taxo.k2d.
  • For example, to use this pre-built database:
  • tar -xzvf eupathDB_kraken2.tar.gz
  • kraken2 --db eupathDB_kraken2 MYSAMPLE.FNA > MYSAMPLE.KRAKEN2

  • (Do not run kraken2-build --build on this folder.)
  • (This database is NOT compatible with Kraken 1)

For more information on Kraken and Kraken 2, see: Kraken's Website and Kraken2's Website

Class Genus Composition * Number of EuPathDB-28 Files Download Uncompressed
AmoebaDB Acanthamoeba, Entamoeba, Naegleria 29 AmoebaDB_Clean.tgz (326 MB) 1.37 GB
CryptoDB Chromera, Cryptosporidium,
Gregarina, Vitrella
11 CryptoDB_Clean.tgz (86.5 MB) 359 MB
FungiDB Ajellomyces, Aspergillus, Candida,
Coccidioides, Cryptococus, Fusarium,
Rhizopus, Saccharomyces, Trichoderma
87 FungiDB_Clean.tgz (931 MB) 3.5 GB
GiardiaDB Giardia, Spironucleus 6 GiardiaDB_Clean.tgz (21 MB) 72 MB
MicrosporidiaDB Anncaliia, Encephalitozoon, Mitosporidia, Nematocida 25 MicrosporidiaDB_Clean.tgz (35 MB) 199 MB
PiroplasmaDB Babesia, Cytauxzoon, Theileria 8 PiroplasmaDB_Clean.tgz (21 MB) 76 MB
PlasmoDB Plasmodium 9 PlasmoDB_Clean.tgz (27 MB) 216 MB
ToxoDB Cyclospora, Eimeria, Hammondia,
Neospora, Sarcocystis, Toxoplasma
30 ToxoDB_Clean.tgz (456 MB) 1.8 Gb
TrichDB Trichomonas 1 TrichDB_Clean.tgz (43 MB) 180 MB
TriTrypDB Leishmania, Leptomonas, Trypanosoma 39 TriTrypDB_Clean.tgz (336 MB) 1.3 GB
Total EuPathDB-Clean 245 2.3 GB 9.1 GB
*The genuses listed for FungiDB and MicrosporidiaDB are a subset of all genuses represented. For full list of genuses contained in these classes, see the publication supplementary table.


The publication associated with the data is located at:
J. Lu, S.L. Salzberg. (2018). "Removing contaminants from databases of draft genomes." PLoS Comput Biol


Jennifer Lu, Ph.D. ( jlu26 jhmi edu )
Steven Salzberg, Ph.D.

Page Updated: 2020/12/01

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