What is the National Center for Genome Analysis Support (NCGAS)?

On this page:

• Overview
• Services
• Impact
• Intellectual merit
• Contacting NCGAS

Overview

The National Center for Genome Analysis Support (NCGAS), established by Indiana University and the Texas Advanced Computing Center (TACC) with funding by the National Science Foundation (NSF), is an innovative service center providing bioinformatics software, expert consultation, and computational resources to life sciences researchers performing genome analysis. Since its inception, the NCGAS has expanded its partnership to include the Pittsburgh Supercomputing Center (PSC) and the San Diego Supercomputer Center (SDSC).

The NCGAS is intended as a general source of software support and services for projects using Mason, Stampede (TACC), Gordon (SDSC), or Blacklight (PSC) for genome analysis research. NCGAS consultants can help life sciences researchers retrieve useful information from vast data sets generated by genome assembly software, large-scale phylogenetic software, and other genome analysis software.

Additionally, through a partnership between IU and Penguin Computing, NCGAS services and support are available to medical researchers using Rockhopper, the Penguin On-Demand HPC Cloud Service hosted by IU. Rockhopper is a large-memory supercomputing cloud appliance equipped with genome analysis and bioinformatics software. For more about IU's on-demand cloud computing service, see Can I purchase cloud computing services at IU? and Penguin Computing's POD IU page.

Access to NCGAS computational and consulting services is awarded to NSF-funded genomics research projects through an allocation process. To request an allocation, submit the NCGAS Allocations Request form. (You'll be asked to provide information about your project's Principal Investigator, your NSF award number, and personal information about each individual who will need an account on NCGAS systems.)

For more, see the NCGAS web site.

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Services

The NCGAS provides the following services:

• Support for users of genome analysis software on Mason, Stampede, Gordon, Blacklight, and Rockhopper (the POD IU resource)
  
  
• Storage of submitted data sets and results (for at least one year following analysis)
  
  
• A repository of open source genome analysis software, including hardened, tuned, and optimized versions of particularly important open source software
  
  
• Support for use of open source genome analysis software, including extended, in-depth consulting for sequence analysis, and tutorials and presentations about using NCGAS services
  
  
• Access to Galaxy, the web-based platform for data-intensive genome analysis research, for researchers with various affiliations:
  
  

  Galaxy instance	Required affiliation	Additional information
  Galaxy @ IU	IU students, faculty, and staff	The Galaxy @ IU portal employs IU's Mason cluster for compute services and the IU Data Capacitor for project storage, and is hosted on IU's Quarry Gateway Web Services Hosting System. Access requires an IU Network ID.
  Galaxy @ NCGAS	Researchers with NCGAS allocations	Access requires an NCGAS allocation; click here to request an allocation.
  Galaxy @ Rockhopper on POD IU	Researchers on the POD IU (Rockhopper) cluster	Rockhopper provides fee-based, on-demand cloud computing service. Access requires purchase of on-demand services, see Can I purchase cloud computing services at IU?
  Galaxy Main	Members of the general public	The public instance, hosted by Penn State University (PSU) and Emory University, is a free resource. Data transfer and data storage are not encrypted; if your project deals with sensitive data, consult your local institutional review board or your project's Principal Investigator before uploading data to this Galaxy server.

  Note: The Galaxy project is supported in part by the NSF, the National Human Genome Research Institute (NHGRI), and PSU's Huck Institutes of the Life Sciences.

NCGAS services particularly support the analysis of next-generation sequencer output in the following categories:

• De novo assembly, which does not use a reference genome and requires that each read be compared to every other to find overlaps
  
  
• Metagenomic projects, which simultaneously sequence the combined genomes in an environmental sample, such as ocean water or the human mouth
  
  
• Resequencing, where a closely related genome has already been completely sequenced and assembled

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Impact

By developing a community of investigators and technologists, and exploring new modalities of provisioning computational resources, such as "on-demand" computing, NCGAS represents a sustainable model for the ongoing and increasing need for sequence analysis.

NCGAS is committed to advancing discovery in genome analysis while promoting the integration of cutting-edge research software tools in education. Disciplinary outreach (i.e., providing new resources and supporting practicing biologists who use them) is a key component of its broader impact.

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Intellectual merit

The services and support provided by NCGAS permit biologists to assemble genomes they could not otherwise assemble using industry-standard methods. NCGAS enables innovative and potentially transformative genomics research by providing tools and services that facilitate new insights and important scientific discoveries.

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Contacting NCGAS

For NCGAS staff contact information, see the UITS/OVPIT staff directory. If you have questions or would like more information, email NCGAS.

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This document was developed with support from National Science Foundation (NSF) grant OCI-1053575. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the NSF.