Please use this identifier to cite or link to this item: https://hdl.handle.net/2440/116644
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Type: Journal article
Title: AffyPipe: an open-source pipeline for Affymetrix Axiom genotyping workflow
Author: Nicolazzi, E.
Iamartino, D.
Williams, J.
Citation: Bioinformatics, 2014; 30(21):3118-3119
Publisher: Oxford University Press
Issue Date: 2014
ISSN: 1367-4803
1460-2059
Statement of
Responsibility: 
Ezequiel L. Nicolazzi, Daniela Iamartino and John L. Williams
Abstract: The Affymetrix Axiom genotyping standard and 'best practice' workflow for Linux and Mac users consists of three stand-alone executable programs (Affymetrix Power Tools) and an R package (SNPolisher). Currently, SNP analysis has to be performed in a step-by-step procedure. Manual intervention and/or programming skills by the user is required at each intermediate point, as Affymetrix Power Tools programs do not produce input files for the program next-in-line. An additional problem is that the output format of genotypes is not compatible with most analysis software currently available. AffyPipe solves all the above problems, by automating both standard and 'best practice' workflows for any species genotyped with the Axiom technology. AffyPipe does not require programming skills and performs all the steps necessary to obtain a final genotype file. Furthermore, users can directly edit SNP probes and export genotypes in PLINK format.https://github.com/nicolazzie/AffyPipe.git.
Keywords: Polymorphism, Single Nucleotide
Rights: © The Author 2014. Published by Oxford University Press. All rights reserved.
DOI: 10.1093/bioinformatics/btu486
Appears in Collections:Aurora harvest 3
Mathematical Sciences publications

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