What is Plantagora?
The pace of genome sequencing promises to continue to accelerate thanks to next-generation sequencing (NGS) technologies that have dramatically reduced the cost of generating large numbers of sequence reads. These new technologies are also in a state of almost continuous change, and with their changing capabilities comes the expansion of the number of strategies for de novo sequencing of plant genomes. Consequently, more scientists are faced with a greater breadth of possible strategies for sequencing their genomes of interest, and very little in the way of tools or data to evaluate the appropriateness of a given strategy. This lack of information results in either the expense of collecting data to evaluate strategies, or more often, the selection of a strategy with very little data to support the choice.
Plantagora leverages existing plant genome sequencing data to develop a web-based plant genome assembly simulation platform. For a given genome, a range of sequencing strategies were simulated and the resulting raw sequencing reads were assembled with appropriate de novo assembly software. The resulting sequence assemblies were evaluated with Plantagora's extensive evaluation metrics, and the results were placed in a context that maximizes the value to the user.
Benefits of the Simulation Platform
Pre-computed results for wide-ranging sequencing strategies on multiple, previously sequenced plant genomes : See the Plantagora Database and the Plantagora Graphing Tool.
Ability to use the system to compare rapidly the effectiveness and feasibility of different sequencing and genome mapping strategies prior to testing an approach in the lab.
Immediate feedback on the quality of the sequence assemblies that may result from a chosen sequencing strategy, based on multiple indices of assembly quality and the predicted overall success of the projec
Immediate feedback on the potential cost of a scenario for a sequencing project.
Planned for the future is a feature that will allow the submission of new, previously untested sequencing schemes to be modeled with the Plantagora pipeline.