title: Software solutions for the livestock genomics SNP array revolution.
abstract: Since the beginning of the genomic era, the number of available single nucleotide polymorphism (SNP) arrays has grown considerably. In the bovine species alone, 11 SNP chips not completely covered by intellectual property are currently available, and the number is growing. Genomic/genotype data are not standardized, and this hampers its exchange and integration. In addition, software used for the analyses of these data usually requires not standard (i.e. case specific) input files which, considering the large amount of data to be handled, require at least some programming skills in their production. In this work, we describe a software toolkit for SNP array data management, imputation, genome-wide association studies, population genetics and genomic selection. However, this toolkit does not solve the critical need for standardization of the genotypic data and software input files. It only highlights the chaotic situation each researcher has to face on a daily basis and gives some helpful advice on the currently available tools in order to navigate the SNP array data complexity.
authors.affiliation: Fondazione Parco Tecnologico Padano (PTP), Via Einstein, Cascina Codazza, Lodi, 26900, Italy.
authors.forename: E L
authors.initials: EL
authors.lastname: Nicolazzi
authors.affiliation: Istituto di biologia e biotecnologia Agraria (IBBA-CNR), Consiglio Nazionale delle Ricerche, Via Einstein, Cascina Codazza, Lodi, 26900, Italy.
authors.forename: S
authors.initials: S
authors.lastname: Biffani
authors.affiliation: Fondazione Parco Tecnologico Padano (PTP), Via Einstein, Cascina Codazza, Lodi, 26900, Italy.
authors.forename: F
authors.initials: F
authors.lastname: Biscarini
authors.affiliation: School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK.
authors.forename: P
authors.initials: P
authors.lastname: Orozco Ter Wengel
authors.affiliation: Fondazione Parco Tecnologico Padano (PTP), Via Einstein, Cascina Codazza, Lodi, 26900, Italy.
authors.forename: A
authors.initials: A
authors.lastname: Caprera
authors.affiliation: Fondazione Parco Tecnologico Padano (PTP), Via Einstein, Cascina Codazza, Lodi, 26900, Italy.
authors.forename: N
authors.initials: N
authors.lastname: Nazzicari
authors.affiliation: Fondazione Parco Tecnologico Padano (PTP), Via Einstein, Cascina Codazza, Lodi, 26900, Italy.|Istituto di biologia e biotecnologia Agraria (IBBA-CNR), Consiglio Nazionale delle Ricerche, Via Einstein, Cascina Codazza, Lodi, 26900, Italy.
authors.forename: A
authors.initials: A
authors.lastname: Stella
mesh_terms: D000818:Animals; D003628:Database Management Systems; D056726:Genetic Association Studies; D005828:Genetics, Population / Q000379:methods; D023281:Genomics / Q000379:methods*; D058751:Livestock / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide; D012984:Software
keywords: genome-wide association studies; genomic selection; imputation; livestock species; management; population genetics; single nucleotide polymorphism