RADIS: analysis of RAD-seq data for interspecific phylogeny

Area of Science:

• Bioinformatics
• Computational Biology
• Genomics

Background:

• Processing Restriction site Associated DNA sequencing (RAD-seq) data for phylogenetic inference can be complex.
• Automated exploration of parameters is crucial for robust phylogenetic analyses.

Purpose of the Study:

• To introduce RADIS, a Perl pipeline designed to streamline RAD-seq data processing.
• To facilitate rapid and automated exploration of parameters for phylogenetic inference.

Main Methods:

• RADIS utilizes Stacks for demultiplexing, PCR duplicate removal, and locus building.
• Custom scripts handle read trimming and sample/locus selection.
• RAxML is employed for phylogenetic tree inference, with flexibility for other software.

Main Results:

• RADIS allows users to process raw Illumina data from demultiplexing to phylogenetic tree inference.
• The pipeline supports exploration of various parameter values within a single analysis.
• Enables thorough investigation of RAD-seq data for phylogenetic studies.

Conclusions:

• RADIS simplifies and automates the analysis of RAD-seq data.
• It provides a flexible platform for parameter exploration in phylogenetic inference.
• The pipeline is available on Linux/Unix platforms with a user manual.