Galaxy  

Galaxy is an open source, web-based platform for accessible, reproducible, and transparent computational biomedical research.  It integrates a large number of popular statistical and bioinformatical tools for genomic sequencing data analysis. 

Accessing Galaxy public server is hindered by the data file size limit, slow speed, as well as data security.  To help USC users to truly take advantage of this powerful platform, we have implemented a local instance on our server in USC's High Performance Computing and Communications (HPCC) as part of the HPCC-NML Bioinformatics Computing Resource.

Galaxy provides a platform for many cutting-edge tools that can be used to perform many types of analysis, particularly for next-generation sequencing (NGS) data:

• Direct retrieval of sequence files from the major genome repositories
• Manipulation of text and various sequence files
• Multiple regression and multivariate analysis
• Various types of NGS data analysis
• SNP/WGA data analysis
• Metagenomic data analysis
• Phenotype association analysis
• more...

To use Galaxy @ HPCC-NML, please follow the instruction on the HPCC-NML Bioinformatics Computing Resource page.  Key steps are:

1. Acquire an HPCC account
2. Request the use of the HPCC-NML Bioinformatics Computing Resource
3. Prepare remote access of the HPCC-NML and transfer data files
4. Submit a Galaxy Access Request Form
5. Use Galaxy @ HPCC-NML

Important note:

• Due to the fact that many NGS analyses often take days to complete, users are required to submit a Galaxy Access Request Form for EACH data analysis project.

Galaxy Tutorials and User Support

• Galaxy Video Tutorials
  
• Galaxy 101: The first thing you should try
• Galaxy Overview 2012
• Galaxy Workshop Materials
• Galaxy RNA-seq Course Materials

• Galaxy Wiki
• Contact Galaxy support team: Galaxy support