AffyPipe: an open-source pipeline for Affymetrix Axiom genotyping workflow

Ezequiel L Nicolazzi; Daniela Iamartino; John L Williams

doi:10.1093/bioinformatics/btu486

AffyPipe: an open-source pipeline for Affymetrix Axiom genotyping workflow

Bioinformatics. 2014 Nov 1;30(21):3118-9. doi: 10.1093/bioinformatics/btu486. Epub 2014 Jul 15.

Authors

Ezequiel L Nicolazzi¹, Daniela Iamartino¹, John L Williams¹

Affiliation

¹ Fondazione Parco Tecnologico Padano, Lodi (LO), 26900, Italy.

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.

Availability and implementation: https://github.com/nicolazzie/AffyPipe.git.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Genotype
Genotyping Techniques / methods*
Polymorphism, Single Nucleotide*
Software*
Workflow