Ready to submit samples? Use these links

To submit a new project or get detailed pricing information, use these links. You'll be given a 6-digit request ID to refer to your request later. Your requests stay here until you're ready to submit samples. You return to this link when you're ready to submit your samples.

1. Log in in the upper right corner with your EID

- Don't have an EID, or haven't submitted a sample to us before? Please go read this page for a short orientation before you get started.

2. Select this link to enter a new project (a.k.a. "job request") (you must log in first - upper right corner)

- See this web page for sample input guidelines.
- For Metagenomics and GBS projects, note that DNA concentrations should be normalized before submission.
- Have a lot of samples? Download this sample submission template (required for jobs with more than 30 samples; optional otherwise)

Latest news

24 Nov 14

To contact the GSAF about a sequencing project, please use the new email alias "gsaf <at> austin.utexas.edu". Emails sent to this address take priority over emails sent directly to the Director or Lab Manager.

25 Sep 14

Scott Hunicke-Smith conducted two "Introduction to NGS at UT" training sessions. Here are the slides from that presentation.

11 Sep 14

Scott Hunicke-Smith presented GSAF updates at the Byte Club meeting. The presentation covers new user-accessible equipment, the NextSeq 500 and HiSeq V4 upgrade, pricing changes, new library prep methods, and new data storage options. Here is a PDF copy of the presentation.

18 Apr 14

Fourierseq failure and replacement status Apr 2014

24 Nov 13

The GSAF is proud to announce several major additions and changes to our service offerings. All are effective immediately, and the costs listed below are for internal UT researchers. We have integrated these new NGS prices into our LIMS job/sample submission system so you will have an accurate price for any platform and prep before you submit your samples.

Gene synthesis (in partnership with ARL) - particularly when you need many distinct mutants. The base price is $0.22/base, but can be significantly lower when creating libraries of mutants. More details are listed below and can be found here. Please contact Randy Hughes for further details (hughes at mail.utexas.edu).
16S rRNA bacterial metagenomics for the standard price of $20/sample including prep and sequencing (plus $200 for projects of less than 176 samples).
Genotyping-by-sequencing for the standard price of $25/sample including sequencing (plus $200 for projects of less than 176 samples).
Lower library prep prices - Thanks to well-validated automation, DNA fragment libraries are now $60/sample (>=8 samples) and directional RNA libraries including poly-A mRNA enrichment are now $130/sample (>= 8 samples). In addition to being less expensive, we have also found fewer sequencing issues with libraries prepared at the GSAF and want to pass that savings on to you.
Lower sequencing prices - our efficiency has improved thanks to hard work in process optimization and automation and we can pass that on to you. The new MiSeq and HiSeq instruments are now functioning smoothly and our queue times have been reduced substantially since this past summer. Both MiSeq instruments are capable of the higher output (20-25 million reads) 2x300 bp Version 3 sequencing chemistry, and both HiSeq 2500's are capable of Rapid (up to 2x150 bp) and High Output ("standard" - up to 2x100 bp) runs.

As always, please let us know if you have any questions, concerns, or comments.

Sincerely,

Scott, Jessica, and all the GSAF staff and Randy Hughes and all the ARL staff.

Getting started

New to the GSAF? Expand here to get started...

Review this self-paced training presentation.
Read this page further to learn what instruments we have and what we're experienced with.
Attend UT's Next-gen sequencing club meetings on the first and third Thursdays of the first month of each semester, 3:00 pm., MBB 2.204 - a great place to start learning about NGS techniques applied to real projects. Sign-up on our mailing list by joining "gsafusers" at UT's list server - just select "subscribe" and enter "gsafusers".
If you want to submit samples for the first time, first get a UT EID if you don't have one, then go to our sample submission section for more info, to check our queues, etc..

Get directions here

Protocols, instruments, computers, and software of the UT GSAF

The GSAF serves a wide array of customers and has gained considerable experience in preparing samples and analyzing data for NGS projects. We have industry-leading platforms and some user-accessible instruments. If you're just considering a project or are ready to sequence, we're here to give you great data quickly and affordably. Click to expand...

The GSAF is housed in approximately 2,000 square feet of controlled-access laboratory space and is an experienced NGS facility. Launched in 2008, the GSAF currently processes over 5,000 NGS samples per year.

Our equipment and capabilities include:

Two Illumina HiSeq 2500 next-generation DNA sequencers and associated peripherals. The HiSeq can generate over 600 gigabases of sequence in an 11-day run or 120 gigabases in a ~1 day rapid run. The GSAF has experience generating small RNA, mRNA, genomic DNA fragment, RAD (including ddRAD), bacterial and fungal metagenomics, and genomic DNA large-insert mate-pair libraries for the Illumina platform.
Two Illumina MiSeq next-generation DNA sequencers and associated peripherals. The MiSeq is intended for lower data output, faster turn-around time projects, or for projects requiring longer read lengths (up to 600 bp per template, as two 300 bp sequences).
Informatic tools and hardware sufficient for analysis of next-generation DNA sequencing data, including:
1. Multiple Dell PowerEdge R900 & R720 servers with 16-32 cores each, with BWA, Bowtie, Shrimp, SOAP, and mapreads aligners, NCBI BLAST, and R/Bioconductor, and several de novo assemblers, sequence editors, and genome browsers.
2. The resources of Lonestar, a 22,656 core supercomputer, and Stampede, a 400,000 core supercomputer, both hosted by UT’s Texas Advanced Computing Center, with 15 petabyte of scratch disk storage.
3. The GSAF has software stacks and experience appropriate to your project and both we and TACC staff can assist you in training your students to use this resource effectively.

Lab protocols we are experienced with:

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

Bioinformatic protocols we are experienced with:

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

Instruments in our lab:

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.

Need Accounts? Here's how you can get an account on the GSAF server

Welcome to the UT GSAF Wiki - a central source of information for next-gen sequencing at UT Austin.

All are welcome to explore. With a UT EID you may also edit and contribute. Please sign up for our user group email to get notifications of upcoming seminars, NGS club meetings, and changes to service. Just hit "subscribe", enter your email address, and "submit". You don't have to be at UT to subscribe.

Reference Pages (GSAF and user contributed)

Browse the wiki:

Software and Reference Genomes

The Software section of the BioITeam wiki site lists software available on the GSAF Server Fourierseq and/or TACC and how to use it. The Reference Genomes and Databases section lists pre-installed reference genomes and their mapping indexes.

Lab Protocols and Oligo Sequences

Lab Protocols and Oligo Sequences are useful if you are designing experiments or preparing your own libraries.

User Project Analysis Pages

Use User Project Pages to work with the GSAF about an ongoing analysis project - user editable, share with your PI! Note that in-process laboratory status updates are not stored here.