RADSex

RADSex identifies sex-specific genomic sequences from Restriction Site-Associated DNA Sequencing (RAD-Seq) data to study sex determination and sex chromosome organization in non-model species.

Key Features:

• Assumption-free sex-marker detection: Detects sex-specific markers without prior assumptions about the type of sex-determination system or the structure of the sex locus.
• Software components: Includes the command-line software radsex and the R package sgtr to perform analyses and generate figures reported in the publication.
• RAD-Seq support: Operates on Restriction Site-Associated DNA Sequencing (RAD-Seq) reads as input data.
• Reproducible analyses: Implements all analyses presented in the foundational paper, enabling reproduction of results and figures.
• Performance: Reported to outperform STACKS in speed, resource usage, and visualization options.

Scientific Applications:

• Sex determination discovery: Identification of sex-specific genomic sequences and sex-determination systems in non-model plant and animal species.
• Oryzias latipes re-analysis: Re-analysis of Japanese medaka (Oryzias latipes) RAD-Seq data revealed a previously unknown Y chromosome polymorphism.
• Comparative screening in fishes: Analysis of RAD-Seq datasets from 15 fish species identified sex-determination systems and sex-specific markers in six species, including five species with previously unknown sex-markers.

Methodology:

The workflow is implemented with Snakemake; inputs and parameters are specified in data/info.tsv and config.yaml, reads are obtained from the NCBI SRA repository, and reference genomes are provided via supplied links.