The Genomic Sequencing and Analysis Facility provides "next-generation" DNA sequencing (NGS) services including sample preparation and sequencing for a wide variety of applications. We have two Illumina HiSeq 2500's and two Illumina MiSeq sequencers, and have operated other next-generation DNA sequencing systems in the past. We have a variety of quality control tools to test library quality and support users who create their own libraries or who wish to outsource this service to the GSAF. The GSAF has a staff of experienced technicians capable of performing many RNA and DNA library preps including directional RNA-seq libraries, small RNA libraries, normalized cDNA libraries, whole genome DNA libraries, enriched DNA libraries (e.g. exome capture libraries), and many other more specialized library types. Our data systems are integrated with the Texas Advanced Computing Center (TACC) supercomputer resources, and we work closely with the CCBB/CSSB Bioinformatics Consulting Group who consult and analyze NGS data.
- Creation of fragment (single-end or paired-end) sequencing libraries for all Illumina next-gen sequencers
- Creation of mate-pair or "jumping" sequencing libraries between 1.5kb and 4kb for Illumina next-gen sequencers
- Creation of RNA-seq libraries from total RNA, small RNA, and immuno-precipitated RNA for Illumina next-gen sequencers
- Creation of amplicon libraries (particularly 16s and ITS regions) for the Illumina next-gen sequencers
- Human exome and custom capture with the Agilent SureSelect, Illumina TruSeq, and Nimblegen SeqCap EZ kits
- Sample and library QC using the Agilent BioAnalyzer, Picogreen and Ribogreen fluorimetry, qPCR, and spectrophotometry
- RNA-seq for transcript abundance, alternative splicing analysis, and variant detection
- SNP/variant analysis
- small RNA abundance and alternative editing analysis
- de novo and reference-guided assembly from fragment, paired-end, and mate-pair data on both DNA and RNA (transcriptomes)
- Whole exome data analysis
- Illumina HiSeq 2500 sequencers (two)
- Illumina MiSeq sequencers (two)
- Illumina NextSeq 500 sequencer (one)
- Covaris S220 Adaptive Focused Acoustic shearing device
- DigiLab HydroShear shearing device
- Agilent BioAnalyzer 2100
- Agilent TapeStation
- Invitrogen Qubit fluorimeter
Computational and software resources
- The GSAF hosts a Dell R720 32-core, 196 GB server with a total of 74 TB local disk dedicated to NGS analysis. Access is available free of charge to all GSAF customers. We maintain a wide range of tools for NGS analysis and assembly on this server. Here are instructions to Getting an account on our server.
- In addition, the GSAF uses and works with the TACC bioinformatics group, supporting tools and applications suitable to the TACC environment.
- Want to get started? Contact us if we can help, or here's some documentation describing how to submit samples to the GSAF.
- Need to start analyzing your data? Get an account on our computational server. New to Unix? Check out some Unix and Perl resources for beginners.