As a licensed Genotyping-by-sequencing (GBS) service provider, the Genomics Center provides cost-effective, high-throughput genotyping to academic and industry scientists world-wide. GBS has gained popularity as a robust, genome-wide SNP discovery method with particular utility for species for which there are no commercially-available targeted reagents.
In all of these methods, the general principle is the same: genomic DNA is digested with restriction enzyme(s), ligated with complementary adaptors, amplified, sequenced, and analyzed for SNP genotypes. A small amount of sequencing provides sufficient coverage for reliable SNP calls because the same reduced representation of the genome is sequenced from sample to sample.
The Genomics Center offers two robust GBS methods that differ slightly in their workflow. One, the in-line method, is based on the Poland protocol which has the barcodes in the adaptors to allow for sample multiplexing after ligation. We offer 376-plex with the in-line method using the PstI + MspI double digest.
The alternative method - and our most routinely used - has common adaptors that contain priming sites for Illumina multiplexing indices, so samples are barcoded during PCR amplification, and then pooled. The main advantages to this method is that it allows for highly multiplexed reactions and also enables us to provide greater restriction enzyme options to our clients.
We have worked extensively with many of the popular GBS plant species using industry standard restriction enzymes, and we can use your previous GBS protocol if you need to merge new data with a previous data set. In addition, we have optimized new GBS protocols for over 30 non-model species, giving researchers a new, low-cost genotyping option for their species. Please see our pilot project page for more information on optimizing a GBS protocol for your species.
List 1: Sample of some of the species our GBS team has worked with.
The Genomics Center offers an end-to-end GBS service starting from DNA extraction through variant calling. Our highly experienced extraction team provides unparalleled high throughput extraction services and are able to customize protocols when needed. Please see our extraction page for pricing and contact information.
In addition, we offer a standard variant calling informatic service for diploid species using the STACKS pipeline at $301.44/analysis plus $1/sample. Deliverables include a GBS report as well as raw demultiplexed fastq files and filtered genotype calls in VCF format. If you are interested in further analyses beyond what is included our standard analysis report, please discuss your project goals with your GBS project manager prior to starting your project. All additional analyses are billed at a rate of $150.72/hour.
Whether your species is new to GBS or has an established protocol, we can help determined which sequencing instrument will best meet your budget and project goals. Clients are encouraged to contact our experienced GBS team for consult on experimental set-up and sequencing options at email@example.com. Please tell us about your project by filling out our GBS project inquiry form to start your project today.
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|GBS Library Creation.|
|Includes DNA sample QC||96-any||sample||$12.16||$16.75|
|Pippin HT Size Selection.|
|NextSeq Sequencing. High Output.||150-bp single-read (1 x 150 SR)||1-any||100 million reads||$885.88||$1,210.74|
|150-bp single-read (1 x 150 SR)||1-any||400 million reads||$3,543.52||$4,842.96|
|NovaSeq Sequencing.1||100-bp single-read (1 x 100 SR)||1-any||375 million reads||$2,036.51||$2,728.71|
|150-bp single-read (1 x 150 SR)||1-any||750 million reads||$4,5073.01||$5,457.42|
|Bioinformatics.2||Standard analysis: variant calling for one species||1-any||diploid species||$244.94 + $1.09/sample||$281.60 + $1.26/sample|
|Analysis and requests beyond variant calling||1-any||hour||$122.47||$140.80|
|Lane fractions are sold in increments of 100 million reads for the NextSeq and 375 million reads for the NovaSeq for GBS services only. A sequencing run proceeds when the entire NextSeq lane or both lanes on the NovaSeq flow cell are filled. Sequencing turnaround is fastest when you purchase a full lane.|
|If you were prviously sequencing 94-plex on one HiSeq 2500 lane with 1 x 100 reads, you were sequencing to ~1.91 million reads/sample.|
1-202 Nils Hasselmo Hall (Minneapolis campus)
1-210 Cancer & Cardiovascular Research Building (Minneapolis campus)
20 Snyder Hall (St. Paul campus)
Please send the tracking information to firstname.lastname@example.org.
University of Minnesota Genomics Center
312 Church St SE, 1-202 Nils Hasselmo Hall
Minneapolis, MN 55455
There are three options for transferring data from the UMGC to clients: delivery to the Minnesota Supercomputing Institute’s (MSI) high-performance file system, download from a secure website, or shipment on an external hard drive. Please indicate your data delivery preference when placing an order for sequencing.
Internal clients and external clients that opt-in to MSI storage have their data released to the client’s MSI group directory on the MSI high-performance filesystem (/home/GROUP/data_release/umgc), from where it can be analyzed using MSI’s high-performance computers or Galaxy system. The data is stored for five years in uncompressed format with read-only permissions to avoid accidental modification, and secure off-site tape backups of the data are maintained for disaster recovery. MSI will charge the client a storage fee for this service.
Internal clients that opt-out of MSI storage and external clients can download their data from a secure website using either a web browser or a command-line download tool, complete instructions are provided in an email from the UMGC. The client’s data is available for download for 30 days, after which the data will be removed from the data download website and the client takes responsibility for storing the data.
External clients may have data shipped on a hard drive purchased by the UMGC and invoiced to the client.
MSI guarantees storage of client data for five years, after which the data can be transferred to tape for long-term storage, contact MSI (email@example.com) for more information.
Data is typically recoverable for up to 5 years. If the external researcher should ever need the FASTQ files re-posted to the data download website or shipped on a hard drive within 5 years from data release, email firstname.lastname@example.org to initiate data recovery. The client will be charged for the cost of recovering the data from tape archive. The UMGC does not provide any guarantee that data can be successfully recovered from tape archive.