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PanPhlAn / Pangenome databases


Pre-processed databases

Pangenome databases are available for more than 400 species, see download page.

If your species of interest is not included, you can create your own project specific database using , read more ...

If you need help, contact us at .


Species Number of reference genomes Download file
Escherichia coli 120
Staphylococcus epidermidis 216
Staphylococcus aureus 227
Bacteroides ovatus 5
Bacteroides fragilis 74
Neisseria meningitidis 185

More species are available here.

After download, decompress and move the 8 species database files to your BOWTIE_INDEXES directory. Or, alternatively, keep files in your working directory.

Example of getting the E. coli database, version 2016

# download

# decompress

# create a variable BOWTIE2_INDEXES containing the database directory (if not exist already)
export BOWTIE2_INDEXES=/your/path/to/PanPhlAn_DB/and/bowtie2_indexes/

# move database files to your database directory
mv panphlan_ecoli16* $BOWTIE2_INDEXES

Batch download of all pre-processed databases (14GB)
Download links are in panphlan/tools/

hg clone
source panphlan/tools/

Next step

Screen your metagenomic samples for species related genes by mapping against the species database.
→ panphlan_map