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angsd-wrapper: utilities for analysing next-generation sequencing data.

Arun Durvasula¹, Paul J Hoffman², Tyler V Kent¹

¹Department of Plant Sciences, University of California, Davis, Davis, CA, 95616, USA.

Molecular Ecology Resources

|August 3, 2016

Summary

This summary is machine-generated.

This study introduces angsd-wrapper, a user-friendly tool for population genetics analysis using high-throughput sequencing data. It simplifies complex analyses like diversity estimation and admixture, improving data exploration for researchers.

Keywords:

Zea domestication population genetics software visualization

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Area of Science:

Population Genetics
Molecular Ecology
Bioinformatics

Background:

High-throughput sequencing (HTS) has revolutionized population genetics and molecular ecology, impacting experimental design and data analysis.
The existing software package, angsd, enables population genetic analyses on HTS data using probabilistic genotype likelihoods, avoiding the need for SNP calling and improving accuracy with low-depth sequencing.
A user-friendly interface is needed to streamline the application of angsd for various population genetic analyses.

Purpose of the Study:

To present angsd-wrapper, a set of scripts providing a user-friendly interface for the angsd software.
To facilitate diverse population genetic analyses, including nucleotide diversity, neutrality tests, principal component analysis, admixture estimation, and introgression quantification.
To enhance data exploration through interactive visualization of angsd results.

Main Methods:

Development of wrapper scripts to interface with the angsd software package.
Implementation of support for multiple population genetic analyses directly from high-throughput sequencing data.
Integration of interactive graphing functionalities for visualizing analysis outcomes.

Main Results:

angsd-wrapper offers a simplified workflow for complex population genetic analyses.
The tool supports a wide range of analyses, from nucleotide diversity to admixture and introgression.
Interactive visualizations aid in the exploration and interpretation of population genetic data.

Conclusions:

angsd-wrapper enhances the accessibility and utility of the angsd software for population geneticists.
The tool simplifies the analysis of high-throughput sequencing data, enabling more accurate and efficient research.
Demonstrated utility in analyzing resequencing data from wild and domesticated Zea populations.