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Important documentation:
Why use ipyrad at all?
- Simple: Easy to install, easy to use.
- Resourceful: Documentation, tutorials, cookbooks, and help forums available.
- Reproducible: Promoting the use of Jupyter Notebooks to organize workflows.
- Flexible: API access to functions and data to build custom assemblies.
- Transparent: Providing human readable code and data files.
Why prefer it to stacks?
- Allow variable length sequences
- Allow for indel variants
- Accomodate PE data coherently
- Multiple reference sequence modes built-in
- Massive parallelization (use as many cores as available)
- Support for more RAD-seq protocols (GBS, 2bRAD, 3RAD, etc)
- ipyrad param file interface and API mode provide a modern UI