ipyrad

ipyrad assembles and analyzes restriction-site-associated DNA sequencing datasets (RAD, ddRAD, and GBS) to enable population genetic and phylogenetic studies.

Key Features:

• Supported data types: Processes RAD, ddRAD, and GBS sequencing data for downstream genetic analyses.
• Assembly approaches: Implements both de novo and reference-based assembly of loci from sequencing reads.
• Scalability: Handles datasets comprising hundreds of taxa and thousands of samples.
• Parallelization: Supports parallel execution on high-performance computing clusters to accelerate processing.
• Implementation: Implemented in Python.

Scientific Applications:

• Population genetics: Enables exploration of genetic variation within and between populations using assembled RAD-seq data.
• Phylogenetic inference: Facilitates inference of evolutionary relationships across taxa from assembled loci.
• Adaptation studies: Supports analyses aimed at investigating species adaptation mechanisms using RAD-seq derived markers.

Methodology:

Performs de novo and reference-based assembly of RAD, ddRAD, and GBS reads and supports parallelized execution on high-performance computing clusters.