A Bacterial Pangenome Analysis Pipeline. Shares information between genomes to correct errors. Can call large structural variants. Fast and scalable to over 10k bacterial genomes.

• Version: 1.3.3
• Added: August, 2023
• Link: https://github.com/gtonkinhill/panaroo

See which versions are available:

$ module avail panaroo

Load one version into your environment and run it:

$ module load panaroo/1.3.3
$ panaroo --version

Note: Please use the ''--t'' option to tell panaroo how many CPU cores it should use. This number should match the number of CPUs you requested in your SLURM batch allocation.

Notes from the sysadmin during installation:

$ cd /tmp
$ git clone https://github.com/gtonkinhill/panaroo -b v1.3.3
$ cd panaroo
$ module load python/3.9
$ sudo mkdir -p /export/apps/panaroo/1.3.3
$ sudo chown aorth:aorth /export/apps/panaroo/1.3.3
$ python3 -m venv /export/apps/panaroo/1.3.3/venv
$ source /export/apps/panaroo/1.3.3/venv/bin/activate
$ pip3 install --upgrade setuptools pip wheel
$ python3 setup.py install
$ sudo chown -R root:root /export/apps/panaroo/1.3.3

See also, the bioconda recipe for panaroo.