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Choice of Next-Generation Sequencing Pipelines

  • F. Del Chierico
  • M. Ancora
  • M. Marcacci
  • C. Cammà
  • L. Putignani
  • Salvatore ContiEmail author
Protocol
Part of the Methods in Molecular Biology book series (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.

Key words

NGS Metagenomics Whole-genome sequencing 16S rRNA gene Gene mapping RNA-seq Library preparation Template preparation NGS platforms 

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • F. Del Chierico
    • 1
  • M. Ancora
    • 2
  • M. Marcacci
    • 2
  • C. Cammà
    • 2
  • L. Putignani
    • 1
  • Salvatore Conti
    • 3
    Email author
  1. 1.Unit of Parasitology & Unit of Metagenomics, Bambino Gesù Children’s HospitalIRCCSRomeItaly
  2. 2.Istituto Zooprofilattico Sperimentale dell’ Abruzzo e Molise “G. Caporale”National and OIE Reference Laboratory for BrucellosisTeramoItaly
  3. 3.Thermo Fisher ScientificMonzaItaly

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