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Galaxy: Overview

Galaxy @ USC

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.

Main Features

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.  The local Galaxy server is currently configured to specialize in ChIP-seq analysis.

  • Cistrome toolbox (MACS, MACS2, CEAS, BETA, etc.)
  • Nebula tools (FindPeaks, ChIPmunk, etc.)
  • SICER, CCAT, IDR, DiffBind
  • more...

Access Galaxy @ USC

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.