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Genomics Compute Cluster on Quest

The Feinberg School of Medicine, in an initiative spearheaded by the Feinberg School of Medicine Office of the Dean, the Center for Genetic Medicine, and the Department of Biochemistry and Molecular Genetics provides 100 nodes on Northwestern’s High Performance Computing Cluster, Quest, to be used for genomics research. This University resource has been made available to the greater genomics community in an effort to foster genomics research and empower the computational genomics community at Northwestern University.

How can I apply to use the genomics nodes?

Principle Investigators (PIs) doing genomics research and their graduate students may apply to use the genomics nodes by completing the Genomics Node User Registration form. In addition to providing their name and NetID, prospective users will be prompted to enter a brief statement of research to be performed on the genomics compute cluster. Once requests are approved, prospective users attend a genomics compute cluster orientation and their NetIDs are added to the Quest buy-in group, b1042.

What is included with access to the genomics compute cluster?

Access to the 100 Genomics Compute Nodes

The 100 nodes of the Genomics Compute Cluster each have 24 cores and 128 GB of memory for a combined resource of 2,400 cores. Submit jobs to these nodes through six different genomics queue options on Quest:

Access to 2 high-memory Nodes

The 2 high-memory nodes each have 28 cores and 1 TB of memory.  Members of the Genomics Compute Cluster may access these nodes by special request.

175 TB scratch in /projects/b1042

Shared storage space for temporary files used when genomics jobs are run. Users are requested to create a PI directory under projects/b1042 to keep scratch files from intermingling with other users’ work. Please keep in mind this is a shared resource and it is important to implement best practices regarding cleaning up these files and using the scratch space in the most efficient way possible, including ending batch files by deleting temporary files that are no longer needed and moving files to your /projects or /home directory when complete.

10 TB shared library space in /projects/genomicsshare

This storage space is read-only and intended to store shared reference files for the use of the genomics research community.  To see a list of files available in genomicsshare, look in /projects/genomicsshare/README.  To request files be added to the shared genomics reference library, email quest-help@northwestern.edu and include genomicsshare in the subject line.

Consulting with the Senior Bioinformatics Specialist

While anyone at Northwestern can consult with Research Computing’s Senior Bioinformatics Specialist, genomics compute cluster users receive orientations, code review, and assistance with parallelizing code. For an appointment, please contact quest-help@northwestern.edu.

Bioinformatics software available on Quest

New software is continually being added to Quest. Users may use the command “module avail” for an up-to-date listing of all software packages including genomics software on Quest. If you would like additional software packages installed on Quest, please contact quest-help@northwestern.edu. Additionally, software can also be installed by users in their own directories.

Software related to genomics on Quest includes:

Bamtools
Basemount
Bedtools
Bismark
Bowtie
BWA
Cytoscape
Eigen
GATK
GeneTorrent
Homer
NGSplot
Picard
Plink
Samtools
SNPtest
STAR aligner
Tophat
VCFtools

How do I Start Using the Nodes?

Please visit the Knowledge Base article.

Join the Genomics Conversation

The genomics nodes on Quest have a Slack community open to anyone with a  Northwestern email address.  Join the Genomics Slack channel at genomics-rcs.slack.com.

Getting help

Learn more about using Quest. If you need more personalized assistance, send an email stating your issue to quest-help@northwestern.edu so the Research Computing Services team may assist you with your issue.

Acknowledgment of Use – Genomics Computing Cluster

This research was supported in part through the computational resources and staff contributions provided by the Genomics Computing Cluster which is jointly supported by the Feinberg School of Medicine, the Center for Genetic Medicine, and Feinberg’s Department of Biochemistry and Molecular Genetics, the Office of the Provost, the Office for Research, and Northwestern Information Technology. The Genomics Computing Cluster is part of Quest, Northwestern University’s high-performance computing facility, with the purpose to advance research in genomics.

Language for Grant Writing purposes 

The PI’s group has access to the University's 800-node high-performance computing (HPC) system Quest, and it’s Genomics Compute Cluster, a 102 node cluster with 2,456 cores total dedicated to genomics research.

The Quest Genomics Compute Cluster architecture includes:
Use of Quest includes system administrative and software support, as well as consultation and user training. Use of the Genomics Compute Cluster on Quest includes software support and training from the dedicated Senior Bioinformatics Specialist from Northwestern IT’s Research Computing Services. The Genomics Computing Cluster and the Senior Bioinformatics Specialist are funded by Northwestern IT, the Feinberg School of Medicine, the Departments of Biochemistry and Molecular Genetics, and the Center for Genetic Medicine in support of genomics research.

Last Updated: 14 December 2017

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