pneumococcal fasta serotyping
- S. pneumoniae in-silico serotype prediction from assembled genome sequences (.fasta)
- Developed by Pfizer.inc
Clone the repository and enter the directory:
git clone https://github.com/PfizerRD/pfaster.git
cd pfaster
Build and activate the environment:
conda env create -f environment.yml
conda activate serotyper
To predict the serotype from a genome sequence:
python pfaster.py -f path_to_fasta_file -o output_file_directory
The -o input is optional. Results will only print to the console if no directory is specified.
Sample genomes are available for testing. For instance:
python pfaster.py -f tests/Pn1_test_ERR1439829.fasta
Test genomes are sourced from the European Nucleotide Archive (ENA, https://www.ebi.ac.uk/ena)
For more information, contact jonathan.lee@pfizer.com