Fill out our GBS inquiry form to tell us about your genotyping needs.


Contact us for project support and questions.

GBS Pilot Projects


Overview

Pilot projects are ideal for species new to GBS or for species with industry standard protocols that want to move away from a frequent-cutter enzyme to improve sequencing costs. The pilot project enables a researcher to validate a sub-set of their sample collection with one double-digest to assess the number of informative markers and to estimate genetic diversity across recovered loci before committing to a full GBS project. The deep sequencing in a pilot project allows for scaling the amount of sequencing of your full sample set based on desired number of SNPs and overall project budget.

GBS workflow
Figure 1: Workflow for optimizing a species for GBS. The pilot project workflow (QC through analysis) and the full project sample prep (QC and norm) operate in parallel to efficiently optimize a GBS protocol.

Because there is not a way to predict the SNP outcome for a given depth of sequencing, nearly all of our GBS clients with new species elect to begin with a pilot project. Pilots are bypassed if a client has a previous GBS data-set with a specific restriction enzyme they have been using for their specie.

Pilot Workflow


Client selects 8 samples that represent the diversity of the population(s), or parents and the offspring of the crosses, to test with one double-digest and sequence deeply to 4 million reads/sample. Restriction enzymes selected are based on in silico digests, or if no reference genome is available, genome size plus the desired number of markers for the study. As with most NGS applications: more markers = more sequencing = greater costs.

Client selects 8 samples that represent the diversity of the population(s), or parents and the offspring of the crosses, to test with one double-digest and sequence deeply to 4 million reads/sample. Restriction enzymes selected are based on in silico digests, or if no reference genome is available, genome size plus the desired number of markers for the study. As with most NGS applications: more markers = more sequencing = greater costs.

Pilot analysis


Oak leaf

Our bioinformatic team will analyze the pilot data three times:

  1. Using the full sequence data at 4 million reads/sample
  2. Sub-sampled down to 2 million reads/sample
  3. At 1 million reads/sample

Pilot deliverables


A full set of deliverables (raw fastQCs, vcf files, and summary report) are provided for each analysis to enable the client to determine which read depth meets their project goals and budget. Once the client verifies the sequencing depth, library prep will begin on the full sample set using the protocol determined in the pilot project.

Pilot timeline


It will take approximately 8-10 weeks for the pilot project’s vcf files and summary report to be released. Running parallel to the pilot project, clients can elect to submit samples for their full GBS project to begin QC and sample normalization.

Start a Pilot


Share with us your species details and genotyping needs using our GBS project inquiry form, and our GBS team will contact you to discuss experimental design.

Pricing

Expand all

Standard

Service Scale Unit UMN External
Pilot project for protocol optimization        

Includes library prep, sequencing, and informatics

1-any

8 samples

$749.82

$1,024.93

Notes

Samples are sequenced deeply to 4 million reads/sample (32 million reads total for the pilot project) and analyzed at 1, 2, and 4 million reads/sample. Client determines the sequencing depth for their full GBS project.

Guidelines

Expand all

Submission

Samples can be dropped-off at one of our laboratory locations.

1-202 Nils Hasselmo Hall (Minneapolis campus)

1-210 Cancer & Cardiovascular Research Building (Minneapolis campus)

20 Snyder Hall (St. Paul campus)

If shipping samples, the following address should be used.

Please send the tracking information to gbs@umn.edu.

University of Minnesota Genomics Center
Genotyping
312 Church St SE, 1-202 Nils Hasselmo Hall
Minneapolis, MN 55455
612-624-3177

Deliverables

Data Release


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.

MSI storage

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.

Web download

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.

Hard drive

External clients may have data shipped on a hard drive purchased by the UMGC and invoiced to the client.

 

Data Recovery


MSI storage

MSI guarantees storage of client data for five years, after which the data can be transferred to tape for long-term storage, contact MSI (help@msi.umn.edu) for more information.

Web download and hard drive

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 next-gen@umn.edu 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.