FL BPHL's core genome SNP pipeline for the identification of clusters of closely related bacterial isolates to support public health surveillance and outbreak investigations.
FL-cgSNP was developed to calculate pairwise cgSNP distances between a group of bacterial isolates to help identify outbreak clusters. The pipeline uses .gff files generated from our FLAQ-AMR pipeline as input. Final outputs include a pairwise cgSNP distance matrix and a maximum likelihood phylogenetic tree. The current version will run only on HiPerGator(HPG) using local Singularity containers for each pipeline process.
Stay tuned for FL-cgSNP's upgrade to Talbot, a platform agnostic Nextflow workflow. Talbot is currently under active development.
- Python3
- Singularity/Apptainer
- Git
To load python3 into your current environment on HiPerGator, either use module load python to get the lastest version of python or activate your base conda environment. For more information on how to set up your base conda environment on HPG, see the HiPerGator Analysis Reference Guide).
Singularity/Apptainer will be loaded as a module during your job execution on HPG using the sbatch job script in this repository.
Git is already installed in your HPG environment upon login.
For first time use, clone this repository to a directory in blue on HPG, such as in /blue/bphl-<state>/<user>/repos/bphl-molecular/.
cd /blue/bphl-<state>/<user>/repos/bphl-molecular/
git clone https://github.com/BPHL-Molecular/fl_cg_snp.git
For future use, update any changes to your local repository on HPG by navigating to the fl_cg_snp repository and pulling any changes.
cd fl_cg_snp/
git pull
To run the FL-cgSNP pipeline, copy all files from the fl_cg_snp local repository to your analysis folder.
mkdir <analysis_dir>
cd <analysis_dir>
cp /blue/bphl-<state>/<user>/repos/bphl-molecular/fl_cg_snp/* .
cp /path/to/gffs/*.gff .
Edit your sbatch job submission script to include your email to receive an email notification upon job END or FAIL. Replace ENTER EMAIL in #SBATCH --mail-user=ENTER EMAIL with your email address. Make sure there is no space between = and your email address. Edit additional sbatch parameters as needed to run your job succesfully, such as the length of time the job will run.
Submit your job.
sbatch sbatch_fl_cg_snp.sh
The main outputs include: pairwise_matrix.tsv; SNPs_boot.treefile.
Please email [email protected] for questions and support.