ADMIXPIPE: population analyses in ADMIXTURE for non-model organisms

Area of Science:

• Molecular Ecology
• Bioinformatics
• Population Genomics

Background:

• Reduced-representation sequencing protocols have advanced molecular ecology for non-model organisms.
• Existing bioinformatic tools often require reference genomes, posing challenges for non-model species.
• There is a need for software to process ADMIXTURE outputs and infer optimal population clusters (K).

Purpose of the Study:

• To develop a bioinformatic pipeline (ADMIXPIPE) for efficient analysis of ADMIXTURE output.
• To facilitate population structure delineation and optimal K-value inference for non-model organisms.
• To provide a user-friendly tool for researchers working with large genomic datasets.

Main Methods:

• ADMIXPIPE filters Single Nucleotide Polymorphisms (SNPs) for ADMIXTURE analysis.
• The pipeline parses ADMIXTURE output for summarization and graphical representation using CLUMPAK.
• Benchmarks demonstrate efficiency in processing double digest restriction-site associated DNA sequencing (ddRAD) data.

Main Results:

• ADMIXPIPE effectively processes large, non-model organism datasets generated by ddRAD.
• The pipeline's outputs are comparable to STRUCTURE and visualize variation across ADMIXTURE runs.
• Facilitates the selection of the most appropriate K-value for population structure analysis.

Conclusions:

• ADMIXPIPE integrates ADMIXTURE analysis with VCF filtering for CLUMPAK compatibility.
• Efficiently analyzes large population genomic datasets from non-model organisms using ADMIXTURE.
• ADMIXPIPE is freely available for Mac OSX and Linux platforms.