RADIS

RADIS automates processing and parameter exploration of RAD-seq Illumina data to build loci catalogs, remove PCR duplicates, select loci and samples, and produce phylogenetic inferences.

Key Features:

• Modular Processing: Handles distinct phases of RAD-seq analysis from demultiplexing to final phylogenetic tree construction, allowing tailored workflows.
• Parameter Exploration: Supports simultaneous exploration of multiple parameter values within a single analysis run, including loci building and sample/loci selection.
• Integration with Established Tools: Leverages Stacks for demultiplexing, PCR duplicate removal, and construction of individual and catalog loci, and incorporates RAxML for phylogenetic inference with the possibility to substitute other compatible software.
• Custom Scripting: Includes scripts for read trimming and loci/sample selection to improve data quality and dataset composition.

Scientific Applications:

• Phylogenetic analyses: Produces loci catalogs and inputs for phylogenetic inference from RAD-seq datasets.
• Population structure and genetic diversity: Supports exploration of genetic diversity and population structure using RAD-seq loci.
• Species relationships: Facilitates analyses of species relationships based on assembled loci and resulting phylogenetic trees.

Methodology:

The pipeline is implemented in Perl for Linux/Unix, processes raw Illumina sequencing data through demultiplexing and PCR duplicate removal via Stacks, performs read trimming and selection of loci and samples, and carries out final phylogenetic inference using RAxML or alternative software.