JCVenterInstitute/CAMRA

CAMRA is a DS-I Africa research hub focused on analyzing clinical and molecular data related to antimicrobial resistance (AMR) in bacterial infections in Nigeria and Rwanda with the aim of translating genomics of AMR to sensitive, rapid diagnostics, and effective therapeutics. # Combatting Antimicrobial Resistance in Africa Using Data Science ## Table of Contents - Introduction - Prerequisites - Installation - Usage - Docker Images - WDL Workflow - Examples - Contributing - License ## Introduction ### About CAMRA CAMRA is a DS-I Africa research hub focused on **analyzing clinical and molecular data related to antimicrobial resistance (AMR)** in bacterial infections in Nigeria and Rwanda with the aim of **translating genomics of AMR to sensitive, rapid diagnostics, and effective therapeutics.** ### About CAMRA's Pipeline A pipeline for the scientist who doesnt want to code. This pipeline is designed to assemble, qc, conduct extensive AMR detection with a viarety of tools, annotation and pangenome analysis, all to fulfill the scientific requirements for CAMRA and **with the intent to be used by other projects**. The pipeline was designed to: - run either: - on Terra.bio (no command line interaction, but requires Terra.bio account) - locally (requires familiarity with command line) - Be modular. Users can decide to run entire pipeline or only sections of the pipeline, such as the AMR worflow/section. - Permit scientist with minimal computational skills the ability to process their bacterial isolates. ## Usage Instructions More detailed instructions can be found on the wiki, including running on TERRA and locally. ## Prerequisites ### Terra.bio Run To run on Terra.bio requires both user account and an active project, both with can be setup according to the steps [HERE] ### Local Run - uses Docker as a container for the different AMR programs - can use Cromwell from the Broad Institute to run terra commands locally Description using exemplar data are shown [HERE] ## What you will find here The repository includes: - Dockerfiles for JCVI-produced and 3rd party bioinformatic tools - Workflows in the Workflow Description Language (WDL) tailored for Terra, a cloud-native research platform. These can also be tested using Cromwell - Exam …