Collectively Improving Robustness and Reproducibility in Genotyping-By-Sequencing (GBS) Experiments

Many researchers have used genotyping-by-sequencing to generate marker data since the method was published in PLoS ONE in 2011. Others have made modifications to the method resulting in different, but related, types of GBS data generated. Additional analysis pipelines have been developed, many of which are licensed under Free / Libre and Open Source licenses -- allowing them to be inspected, tested and improved upon. Taken together these modifications and analysis pipelines demonstrate the power of the scientific method when combined with modern genomics laboratory techniques, open access publishing and open source software to rapidly and democratically advance our ability to conduct research. It has also left researchers wanting to use the technology with several questions which need to be answered before they adopt the approach. First, what laboratory method should one use to make GBS libraries? Second, what sequencing platform should be used and how? Third, what pipeline is best suited for the data generated and the genetics of the system being studied?

A group of like-minded scientists has come together to build software tools and an information repository to help others answer these questions for their own experiments in a project called Biospectra-by-Sequencing. The aim of the project is developing an informational Wiki for geneticists and genomicists as well as a containerized software test rig to evaluate and run many GBS pipelines. We describe the status of the project, how to access the work we have done so far and how researchers can participate in the BBS project.