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1 Introduction

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Ezequiel L. Nicolazzi edited this page Jul 5, 2016 · 5 revisions

##1.A. WHAT IS ZANARDI? Zanardi is a pipeline written with the objective to make life easier for people dealing with genomic data. Usually, format conversions are difficult to handle, and many software have different requirements and dependencies. This, together to a large number of other difficulties, makes software integration unstable and streamlining multiple software difficult. Zanardi is an all-in-one tool, user-friendly and completely open-source that tries to tackle all the above. This pipeline heavily relies on multiple-purpose software coded by other researchers, so please make sure you acknowledge their work while running Zanardi. See the “How to cite Zanardi” section for full information and links to the original software. From the user side, you’re expected to be perfectly aware of what your objectives are and what you expect as a result. Running Zanardi without a good knowledge of the underlying software is a great risk, so please use this tool wisely. In fact, although this pipeline helps users make things in an easy(er) way, users are still highly encouraged to read the manuals of each software streamlined here.

##1.B. WHY “ZANARDI”? The name of this tool is inspired to our personal hero: Alex Zanardi ( http://en.wikipedia.org/wiki/Alex_Zanardi), an outstanding person, a racing champion, a Paralympic gold medalist and a true ironman, among other qualities. Although his life is a great inspiration per se, this tool was named upon him because we wanted something that was fast, robust and that could help people overcome the struggle of... genomic analyses. Pretty close to someone like him! If you are interested in knowing more about his inspiring life, you should read the book: "Alex Zanardi: My Sweetest Victory". You won’t regret it.

##1.C. ZANARDI FOR WINDOWS USERS Zanardi can be used also by Windows users.. with just a few tricks. Users should install a linux virtual machine (don't worry, it's not THAT difficult), and install git and R in it. This will take ~1 hour of your time, but the benefits are AWESOME! :-) A step-by-step guide is provided here. Slides of a step-by-step example of the use of Zanardi (and some other software) can be found here.

##1.D. HOW TO CITE ZANARDI If you find this software useful, please cite:

  • Marras G., Rossoni A., Schwarzenbacher H., Biffani S., Biscarini F., Nicolazzi E.L. (2016) Zanardi: an open-source pipeline for multiple-species genomic analysis of SNP array data. Animal Genetics (in press)

##1.E. WHO ARE WE? Gabriele Marras is a post-doc researcher at Parco Tecnologico Padano (PTP), Italy.

Attilio Rossoni is the head of R&D at ANARB (Italian Brown Swiss Breeders Association), Italy.

Hermann Schwarzenbacher is a reserarcher at the R&D office of ZuchtData GmbH, Austria.

Stefano Biffani is a Research fellow (Geneticist/Biostatistician) at IBBA-CNR National Research Council

Filippo Biscarini is a Principal investigator in Bioinformatics, Bioistatistics and Biomedicine at Parco Tecnologico Padano (PTP), Italy.

Ezequiel L. Nicolazzi is the Technical manager of the Bioinformatics core facility of Parco Tecnologico Padano (PTP), Italy.

##1.E. ACKNOWLEDGMENTS The research leading to these results has received funding from the European's Union Seventh Framework Programme for research, technological development and demonstration under grant agreement 289592 - Gene2Farm (www.gene2farm.eu), from the FACCE-ERA-NET ClimGen project and from the Italian research project “GenHome”.

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