PanAdapt is a Nextflow Pipeline designed to perform positive selection analysis on bacterial genomes. PanAdapt accepts genomes in fasta format as input and performs gene-level positive selection analysis using BUSTED and site-level positive selection analysis using FUBAR.
PanAdapt is available via github
git clone https://github.com/rki-mf1/PanAdapt
PanAdapt depends on conda for environment management. Please ensure that a version of conda is available on your system. PanAdapt was extensively tested with miniconda. The miniconda installation guide can be found here. Using conda install and activate the PanAdapt environment with the following commands:
conda env create -f environment.yml
conda activate PanAdapt
This environment contains the packages nextflow and bakta. Now download a collection of databases for genome annotation with bakta using the following command:
bakta_db download --output resources --type light
Run the pipeline locally using the following command:
nextflow run main.nf --input_genomes path/to/genomes.fasta -profile local,conda
Or run the pipeline via sbatch with the following command:
nextflow run main.nf --input_genomes path/to/genomes.fasta -profile slurm,conda
By default all output are saved to the results directory in the base directory. Final results for the gene-level analysis can be found in the directory extract_ppanggolon_results and final results for site-level analysis are stored in the calculate_shannon_entropy directory.