What does ipyrad do?¶
ipyrad is a toolbox for assembly and analysis of RAD-seq type genomic data sets. Notably, it has four assembly methods by which to assemble data: denovo, reference, reference addition, and reference subtraction. Assembled data sets are created in a variety of output formats, facilitating downstream genomic analyses for both population genetic and phylogenetic studies. ipyrad also includes methods for visualizing and analyzing data and results.
How is it different from pyrad?¶
ipyrad is a complete re-write of pyrad with an expanded focus on speed and flexibility. While we continue in the minimalist ethos of pyrad, which emphasized a simple installation procedure and ease-of-use, ipyrad offers many new features, and is now easily extensible to new data types and models through its Python API.
Major New Features in ipyrad¶
- New assembly methods: de novo and reference-based methods.
- Improved checkpointing. Interrupted jobs are easily restarted.
- Much faster code (speed comparisons forthcoming with publication).
- State of the art parallel implementation (ipyparallel) for running on computing clusters.
- Easy installation: all dependencies are included during installation.
- Downstream analysis tools
- Quartet-based species tree inference (_tetrad_ program)
- Introgression analyses (ABBA-BABA tests)
- Population genetic statistics