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Choice of Next-Generation Sequencing Pipelines

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Bacterial Pangenomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1231))

Abstract

The next-generation sequencing (NGS) technologies are revolutionary tools which have made possible achieving remarkable advances in genetics since the beginning of the twenty-first century. Thanks to the possibility to produce large amount of sequence data, these tools are going to completely substitute other high-throughput technologies. Moreover, the large applications of NGS protocols are increasing the genetic decoding of biological systems through studies of genome anatomy and gene mapping, coupled to the transcriptome pictures. The application of NGS pipelines such as (1) de-novo genomic sequencing by mate-paired and whole-genome shotgun strategies; (2) specific gene sequencing on large bacterial communities; and (3) RNA-seq methods including whole transcriptome sequencing and Serial Analysis of Gene Expression (Sage-analysis) are fundamental in the genome-wide fields like metagenomics. Recently, the availability of these advanced protocols has allowed to overcome the usual sequencing technical issues related to the mapping specificity over standard shotgun library sequencing, the detection of large structural genomes variations and bridging sequencing gaps, as well as more precise gene annotation. In this chapter we will discuss how to manage a successful NGS pipeline from the planning of sequencing projects through the choice of the platforms up to the data analysis management.

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Author information

Authors and Affiliations

  1. Unit of Parasitology & Unit of Metagenomics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy

    F. Del Chierico & L. Putignani

  2. Istituto Zooprofilattico Sperimentale dell’ Abruzzo e Molise “G. Caporale”, National and OIE Reference Laboratory for Brucellosis, Teramo, Italy

    M. Ancora, M. Marcacci & C. Cammà

  3. Thermo Fisher Scientific, Via. G. B. Tiepolo 18, 20900, Monza, Italy

    Salvatore Conti

Authors
  1. F. Del Chierico
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  2. M. Ancora
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  3. M. Marcacci
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  4. C. Cammà
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  5. L. Putignani
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  6. Salvatore Conti
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Corresponding author

Correspondence to Salvatore Conti .

Editor information

Editors and Affiliations

  1. Department of Biology, University of Florence, Florence, Italy

    Alessio Mengoni

  2. EMBL-EBI, Cambridge, United Kingdom

    Marco Galardini

  3. Department of Biology, University of Florence, Florence, Italy

    Marco Fondi

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Del Chierico, F., Ancora, M., Marcacci, M., Cammà, C., Putignani, L., Conti, S. (2015). Choice of Next-Generation Sequencing Pipelines. In: Mengoni, A., Galardini, M., Fondi, M. (eds) Bacterial Pangenomics. Methods in Molecular Biology, vol 1231. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1720-4_3

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  • DOI: https://doi.org/10.1007/978-1-4939-1720-4_3

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-1719-8

  • Online ISBN: 978-1-4939-1720-4

  • eBook Packages: Springer Protocols

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