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Simple, rapid and accurate genotyping-by-sequencing from aligned whole genomes with ArrayMaker.

ABSTRACT: Whole-genome sequencing has revolutionized the study of genetics. Genotyping-by-sequencing is now a viable method of genotyping, yet the bioinformatics involved can be daunting if not prohibitive for some laboratories. Here we present ArrayMaker, a user-friendly tool that extracts accurate single nucleotide polymorphism genotypes at pre-defined loci from whole-genome alignments and presents them in a standard genotyping format compatible with association analysis software and datasets genotyped on commercial array platforms. Using this tool, geneticists with only basic computing ability can genotype samples at any desired list of markers, facilitating genome-wide association analysis, fine mapping, candidate variant assessment, data sharing and compatibility of data sourced from multiple technologies.ArrayMaker is licensed under The MIT License and can be freely obtained at https://github.com/cw2014/ArrayMaker/. The program is implemented in Perl and runs on Linux operating systems.Supplementary data are available at Bioinformatics online.cali.willet@sydney.edu.au.

SUBMITTER: Willet CE

PROVIDER: S-EPMC4325546 | biostudies-literature | 2015 Feb

REPOSITORIES: biostudies-literature

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Simple, rapid and accurate genotyping-by-sequencing from aligned whole genomes with ArrayMaker.

Willet Cali E CE Haase Bianca B Charleston Michael A MA Wade Claire M CM

Bioinformatics (Oxford, England) 20141021 4

<h4>Summary</h4>Whole-genome sequencing has revolutionized the study of genetics. Genotyping-by-sequencing is now a viable method of genotyping, yet the bioinformatics involved can be daunting if not prohibitive for some laboratories. Here we present ArrayMaker, a user-friendly tool that extracts accurate single nucleotide polymorphism genotypes at pre-defined loci from whole-genome alignments and presents them in a standard genotyping format compatible with association analysis software and dat ...[more]

PMID: 25336502

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Dataset Information

Simple, rapid and accurate genotyping-by-sequencing from aligned whole genomes with ArrayMaker.

Publications

Simple, rapid and accurate genotyping-by-sequencing from aligned whole genomes with ArrayMaker.

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