ybdong919 / pfaster

pneumococcal FASTA serotype calling

PfaSTer

pneumococcal fasta serotyping

• S. pneumoniae in-silico serotype prediction from assembled genome sequences (.fasta)
• Developed by Pfizer.inc

Installation

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

Usage

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.

Tests

Sample genomes are available for testing. For instance:

python pfaster.py -f tests/Pn1_test_ERR1439829.fasta

Additional

Test genomes are sourced from the European Nucleotide Archive (ENA, https://www.ebi.ac.uk/ena)

For more information, contact [email protected]