Welcome To Staphopia

About Staphopia

Staphopia is a database focusing on the genomes of the bacterial pathogen Staphylococcus aureus. Life-threatening Methicillin-resistant S. aureus (MRSA) infections strike across our society, both in the community and hospital settings. In recent years whole genome shotgun sequencing of clinical isolates has become common. As of August 2017 there were over 44,000 publicly available S. aureus sequencing projects in EBI's ENA database. Staphopia aims to provide rapid analysis of these whole-genome datasets as well as useful S. aureus specific results, such as genotype, antibiotic resistance and virulence gene profiles.

Users can create an account to access a basic summary of results for each public sample through this site. Another option, is to access our web API with the use of our R package. For those interested in processing their own data, we have made both the Staphopia analysis pipeline and web application publicly available on GitHub (see below). We have also created a Docker image to simplify the installation process both locally and in the cloud. Also much of the Staphopia pipeline can be used a template for other organism-specific databases.

An Overview of Staphopia

Staphopia Resources

GitHub

Staphopia-R
An R package to query Staphopia's API
Staphopia-AP
Staphopia's analysis pipeline (Dockerized)
Staphopia-Web
Staphopia's Django powered web application

Documentation

API Documentation
Learn more about Staphopia's web API.

Acknowledgements

Staphopia was created by Robert Petit and Tim Read at Emory University School of Medicine in Atlanta Georgia, USA. We would like to thank Colleen Kraft, Tauqeer Alam, Santiago Castillo, Nikolay Braykov, Signe White, Michelle Su, Michael Frisch, Jim Hogan, King Jordan and Jim Heitner for help in putting together Staphopia. We acknowledge (and are grateful) for data from these sources: EBI's ENA, MIGS/MINS, S. aureus MLST, ARDB, StaphVar, and SCCmec.

Thanks also to those researchers and institutions who have contributed published and unpublished sequence public information in to the SRA databases. View Top 10 Contributers. If you would like to stay informed about the progress and improvements of Staphopia, we encourage you to contact us.

Funding

Funding for this study from Emory University, Amazon AWS in Education Grant Program, and NIH grants AI091827 and AI121860.