ANGSD-wrapper

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1 Department of Plant Sciences, University of California, Davis, Davis, California, United States
2 Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, United States
3 Center for Population Biology and Genome Center, University of California, Davis, Davis, California, United States
DOI
10.7287/peerj.preprints.1472v1
Published
Accepted
Subject Areas
Bioinformatics, Evolutionary Studies, Genetics, Genomics
Keywords
software, population genetics, genotype likelihood
Copyright
© 2015 Durvasula et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.
Cite this article
Durvasula A, Kent TV, Hoffman PJ, Liu C, Kono TJY, Morrell PL, Ross-Ibarra J. 2015. ANGSD-wrapper. PeerJ PrePrints 3:e1472v1

Abstract

High throughput sequencing has changed many aspects of population genetics, molecular ecology, and related fields, affecting both experimental design and data analysis. The software package ANGSD allows users to perform a number of population genetic analyses on high-throughput sequencing data. The package is specifically designed to produce more accurate results for samples with low sequencing depth, but it handles a wide array of sampling and experimental designs and makes use of full genome data. Here we present ANGSD-wrapper, a user-friendly interface to ANGSD. ANGSD-wrapper includes a number of ’wrapper’ scripts that facilitate configuration and execution of multi-step analyses. ANGSD- wrapper also provides interactive graphing of ANGSD results, thus enhancing data exploration. We demonstrate the usefulness of ANGSD-wrapper by analyzing resequencing data from populations of wild and domesticated Oryza. ANGSD-wrapper is freely available from https://github.com/ arundurvasula/angsd- wrapper.

Author Comment

This is a preprint submission to PeerJ.