This software is for the inference of beta-lactam resistance phenotype from the PBP genotype of Streptococcus pneumoniae.
This is a fork of the Pathogenwatch's Docker container which is a modified version of AMR predictor by Ben Metcalf at the Centre for Disease Control (CDC). Please credit the original authors in any resulting publication.
Pathogenwatch's Docker container is used as a Docker Executable Image. This version provides a Docker enviornment, which is designed for integrating into the GPS Unified Pipeline (a Nextflow Pipeline for processing Streptococcus pneumoniae sequencing raw reads).
We do not provide any support for the use or interpretation of this software, and it is provided on an "as-is" basis.
In the root directory of the repository run the following command:
docker build -t spn_pbp_amr .
When the built Docker image is set as the container of a Nextflow process, the software can be ran as following
spn_pbp_amr /path/to/assembly.fa > result.json
It will read the assembly from the provided path and output to result.json