cgPhylo is a tool for determining phylogeny between bacterial isolates for which there are core genome MLST schemas (cgmlst.org). Phylogeny is determined by comparing the multiple alignments of conserved core genes shared by the input samples.
To install cgPhylo run:
conda install -c genomicepidemiology cgphyloThe most convenient way (by far) to use this tool is to download the pre-indexed database (Current version indexed from december 22nd 2023 cgMLST scheme):
wget https://cge.food.dtu.dk/services/cgphylo/cgmlst_db.tar.gz
tar -zxvf cgmlst_db.tar.gz
Alternatively, if you want the newest cgMLST schemes, you can follow these step and setup the database yourself (The database indexing may take several hours, so consider doing it in a detached screen session):
1.) Download all the cgMLST schemes from the cgMLST website (https://www.cgmlst.org/ncs). For Burkholderia mallei only download the FLI scheme and make sure to rename the folder to Burkholderia_mallei_cgMLST_alleles. 2.) Place all the folders folder and create a tar ball of all the folders.
tar -zcvf cgMLST_schemes.tar.gz cgMLST_schemes
3.) run the setup_databases.py script found in the scripts folder. This will create the database and index it. Note: If this doesn't work, it may be because of a new update to the cgMLST databases which we have not accounted for. Please raies an issue on Github in that case, and we will fix it.
python3 scripts/setup_databases.py -i cgMLST_schemes.tar.gz -o cgMLST_db
cgphylo --nanopore /complete/path/to/input_files/*.fastq.gz --o any_output_name --threads <int, default:4> --db_dir /path/to/cgmlst_dbApache License 2.0
Malte B. Hallgren