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The goal of this document is to guide you through the process of annotating and characterizing transposons with Tephra. I'll go through a bit of the theory and motivation for the project, and ultimately demonstrate how to characterize the nature of transposons in terms of abundance, diversity, age, and structure.
The code side of this project is now stable and nearly feature-complete, and all of the commands are documented and tested. Though, the full documentation, which you are reading, is just taking shape. This document will grow into a manuscript in the near future. Please don't hesitate to file issues or send me a message if you have any questions about this project.
- Background (the problem of TE characterization)
- Overview (the novel features of Tephra)
- Full demonstration (working examples for model species)
- Comparison of Tephra to published results
Below you will find an overview of the development status and mission of this project.
To contribute or simply view the progress, see the TODO file in the root of the distribution.
All development happens on the /develop topic branches. The goal is for master to always pass the test suite, so please keep this in mind when adding features or bug fixes. Also, where possible, every new feature/command should have a new test file.