Resources

Experimental design and troubleshooting

  • Before starting any genomic sequencing study, we recommend consulting with the biostatistician, computational biologist or bioinformatics experts who will be analyzing the data.  There is no substitute for a well-designed study prior to generating the data. If help is needed, set up an initial review with the Bioinformatics Consulting Group (BCG, bcg@utgsaf.org ) in the Center for Computational Biology and Bioinformatics. 
  • Bringing years of experience with the Illumina sequencing platform, the GSAF staff is available to talk about the technical aspects of library construction, sample quality control run types and sequencing.
  • Need help troubleshooting problems with the “Sanger” DNA sequencing reads? Contact us at dsfcore@austin.utexas.edu; or call 512-475-7844.

Computing, data storage and analysis

  • Texas Advanced Computing Center (TACC). UT investigators have access to TACC’s supercomputers, including Lonestar 5, with 30,000 processor cores, 5-petabyte disk array system and the flagship Stampede 2, a 18-PF peak performance system currently with 4200 Knights Landing (KNL) nodes and more to come.
  • The Biomedical Research Computing Facility (BRCF) hosts the GSAF POD for local high-performance computing and data storage.  The facility provides access to computational tools and hardware sufficient for analysis of large-scale sequencing data. 

POD Specs: Two local compute clusters consist of multiple Dell PowerEdge R720 servers with 24 cores and 196 GB memory.  A data storage server with 24X4-TB Seagate/Western Digital drives delivers 96 TB raw capacity storage, which is managed via the ZFS file system for a net capacity of ~60TB.   The compute cluster is loaded with BWA, Bowtie, and other aligners, NCBI BLAST, and R/Bioconductor, and de novo assemblers, sequence editors, and genome browsers. 

  • Archival storage of all GSAF sequencing run FASTQ files are stored in duplicate at UT’s TACC.  Contact the BRCF to request an account

Training and community

  • The Bioinformatics Team (BioITeam) is a collective of bio-computing scientists at the University of Texas with contributing scientists from TACC, CCBB, GSAF and CSSB.  Tap into the community’s wiki pages for discussions on related topics and training materials.