# Acanthophis

A reusable, comprehensive, opinionated plant variant calling pipeline in Snakemake

Until I write the documentation, please see [the example workflow](example/).
It should contain a fully working example workflow.

![Acanthophis, the most beautiful and bad-ass of snakes](.github/logo.jpg)

## About & Authors

This is an amalgamation of several pipelines developed between the [Weigel Group, MPI DB, Tübingen, DE](https://weigelworld.org), the [Warthmann Group, IAEA/FAO PBGL, Seibersdorf, AT](http://warthmann.com) and the [Borevitz Group, ANU, Canberra, AU](https://borevitzlab.anu.edu.au). This amalgamation authored by Dr. K. D. Murray, original code primary by K. D. Murray, Norman Warthmann, and Ilja Bezrukov, with contributions from others at the aforementioned institutes.


# TODO:

- [ ] break out more freebayes parameters to the config file
- [ ] `acanthophis init` to generate boilerplate
