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, more than 40,000 S. aureus sequencing projects publicly available from EBI's ENA database, have been processed with Staphopia on the Cancer Genomics Cloud platform. 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 (more details below). We have created a Docker image to simplify the installation process both locally and in the cloud. There are also public Staphopia Apps available through the Cancer Genomics Cloud platform.

Staphopia has been published in PeerJ under the title: Staphylococcus aureus viewed from the perspective of 40,000+ genomes .


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

Prebuilt Tools

Public Staphopia analysis pipeline CGC Apps
The same apps used to process 40,000+ genomes on the Cancer Genomics Cloud platform.
Staphopia Analysis Pipeline on DockerHub
Staphopia's analysis pipeline hosted on DockerHub. The tag 20190306 is the tag version that should be used.1

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 Tauqeer Alam, Jim Hogan, Santiago Castillo-Ramírez, Michelle Su, Michael Frisch and Erik Lehnert for their helpful suggestions. We acknowledge (and are grateful) for data from these sources: EBI's ENA, MIGS/MINS, PubMLST, MEGARes, VFDB, 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Thanks also to those researchers and institutions who have contributed published and unpublished sequence public information in to the SRA databases.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.

Finally many thanks and gratitude to the authors of the software programs used in Staphopia's analysis pipeline.


Funding

Funding was from Emory University, Amazon AWS in Education Grant Program, Emerging Infections Program (EIP) grants CDC-RFA-CK12-120903PPHF14 and U50CK000485, and NIH grants AI091827 and AI121860. The Seven Bridges NCI Cancer Genomics Cloud pilot was supported in part by the funds from the National Cancer Institute, National Institutes of Health, Department of Health and Human Services, under Contract No. HHSN261201400008C.


Citation

Petit RA III, Read TD. 2018. Staphylococcus aureus viewed from the perspective of 40,000+ genomes. PeerJ 6:e5261 https://doi.org/10.7717/peerj.5261