The ipyrad command line interface (CLI) is accessed through a terminal. Use the -help (-h) flag to print a help screen with a description of the main arguments to the CLI. Detailed instructions are available through the tutorials below.
>>> ipyrad -h---------------------Start here to learn the basics. We run through an example simulated single-end RAD-seq data set and give detailed descriptions of files and statistics produced by each step of an assembly. Next, try some advanced methods, like using branching to assemble data sets under a range of parameter settings, and assemble data with respect to a reference genome.
Empirical examples -----------------The following tutorials demonstrate assemblies of publicly available empirical data sets representing different data types. The first analysis (Eaton and Ree, 2013) can be assembled very quickly, and is re-used in our analysis cookbook recipes, below. The others include tips for optimizing ipyrad for use with that data type.
- Pedicularis CLI (command line)
- Pedicularis API (run in jupyter-notebook)
- Finch API (run in jupyter-notebook)
- see more ipyrad API cookbooks here