1. Computational Metagenomics Lab
  2. Untitled project
  3. PanPhlAn


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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 panphlan_pangenome_generation.py , read more ...

If you need help, contact us at panphlan-users@googlegroups.com .


Species Number of reference genomes Download file
Escherichia coli 120 ecoli16.zip
Staphylococcus epidermidis 216 sepidermidis16.zip
Staphylococcus aureus 227 saureus16.zip
Bacteroides ovatus 5 bovatus16.zip
Bacteroides fragilis 74 bfragilis16.zip
Neisseria meningitidis 185 nmeningitidis16.zip

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
wget https://www.dropbox.com/sh/rfwb4i9m8s40iba/AAC4mIlAvNKKtC1x-5tIe93Aa/panphlan_ecoli16.zip

# decompress
unzip panphlan_ecoli16.zip

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

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

hg clone https://bitbucket.org/CibioCM/panphlan
source panphlan/tools/download_all_databases.sh

Next step

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