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 subset 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 the desired number of SNPs and the overall project budget.

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

Our bioinformatics 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.