Illumina Sequence Data: RTA, SLIMS and Data Storage
The sequencing data will be converted into bcl basecall files in real time and further converted into FASTQ files using the Illumina bcl2fastq software after the run. The high quality of the data will be verified using the Illumina SAV viewer; this includes verifying low error rates based on alignments of the standard Illumina PhiX spike-in.
Sequencing Data Download: SLIMS
Following analysis of each run, users have access to parsed output through the SLIMS server created in conjunction with the Bioinformatics Core (to get some idea of the look of this interface, login here and use ‘email@example.com’ as the email and ‘slimsdemo’ as the password). A SLIMS account will be created for you on your first run, with information about how to set up and access your account distributed via email. The main SLIMS page can be reached here.
Demultiplexing of sequencing data for standard Illumina Truseq-style and Nextera-style indices is provided as part of the normal service. We will store processed data free of charge for three months – after this time data will be deleted unless you indicate otherwise on the sample submission form or via communication with us.
For the UNIX-savvy user it is possible to use rsync to acquire all your non-image data directly. Please go to here to read how and additional informtion about Bioshare. The Bioinformatics Core is continually gaining expertise manipulating and analyzing these large sequence data sets, so for any assistance downstream of the initial basecalling these are the people to talk to.
We can provide you with access to GenomeStudio for Infinium microarray data.
The Genome Center Bioinformatics Core
Our neighbors from the Bioinformatics Core carry out sequence data analysis, statistical evaluations, consulting, and training to help you get the most out of your data.
Please contact us for complete analysis packages including sequencing and bioinformatics (e.g. differential gene expression, pathway analyses, variant calling) as well as for joint consultations with us and the Bioinformatics Core staff.
Please consider a consultation especially during the planning stage of a new project (free of charge).
Other Analysis Options / Bioinformatics Tools
For the do-it-yourselfer, many open-source tool options exist to carry out analyses on Illumina sequence data. The vast majority of these tools require the use of the command line and of UNIX/Linux operation systems. One exception is the Unipro UGENE suite of tools (http://ugene.net/) available for windows, mac, and linux, which is operated through a graphical user interface. GALAXY is a web-based platform with a simple user interface that can help with many routine workflows. For limited data sets, the USEGALAXY service allows you to analyze data on their servers. Please note that the Bioinformatics Core offers GALAXY workshops and that a UC Davis GALAXY server is in beta-testing.
A search in the OmicTools directory provides likely the easiest way to find the right tool for your bioinformatic tasks. Another good way to find your bearings is to ask in the SEQANSWERS forum.
Worth mentioning is the BBtools suite of command line programs which is developing into a “swiss-army-knife” of bioinformatics. All the tools in there are fast and provide comprehensive reports and statistics on the resulting data.
The Small-RNA Workbench tool suite is very helpful for miRNA data analysis.
The section below is not intended to provide a comprehensive list of sites offering such software, but instead presents some of the tools developed and used by researchers here at the Genome Center :
- The UC Davis Bioinformatics Core has written a suite of open-source bioinformatics software that is freely available here which enables adapter trimming, QC of sequencing data &demultiplexing.
- The Michelmore lab has developed a series of tools for processing and visualizing Illumina data. The site to visit is:
- The Comai lab Barcoded-Data-Preparation-Tools are very helpful for all kinds of de-multiplexing (both in-line barcodes and index-read barcodes) and read-filtering and trimming tasks.