MetaShot: An accurate workflow for taxon classification of host-associated microbiome from shotgun metagenomic data

B. Fosso, M. Santamaria, M. D'Antonio, D. Lovero, G. Corrado, E. Vizza, N. Passaro, A. R. Garbuglia, M. R. Capobianchi, M. Crescenzi, G. Valiente, G. Pesole

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

Shotgun metagenomics by high-throughput sequencing may allow deep and accurate characterization of host-associated total microbiomes, including bacteria, viruses, protists and fungi. However, the analysis of such sequencing data is still extremely challenging in terms of both overall accuracy and computational efficiency, and current methodologies show substantial variability in misclassification rate and resolution at lower taxonomic ranks or are limited to specific life domains (e.g. only bacteria). We present here MetaShot, a workflow for assessing the total microbiome composition from host-associated shotgun sequence data, and show its overall optimal accuracy performance by analyzing both simulated and real datasets.

Original languageEnglish
Pages (from-to)1730-1732
Number of pages3
JournalBioinformatics
Volume33
Issue number11
DOIs
Publication statusPublished - Jun 1 2017

Fingerprint

Metagenomics
Workflow
Microbiota
Firearms
Bacteria
Sequencing
Work Flow
Misclassification Rate
Computational efficiency
Fungi
Viruses
Computational Efficiency
High Throughput
Virus
Throughput
Methodology
Chemical analysis
Datasets
Life

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

MetaShot : An accurate workflow for taxon classification of host-associated microbiome from shotgun metagenomic data. / Fosso, B.; Santamaria, M.; D'Antonio, M.; Lovero, D.; Corrado, G.; Vizza, E.; Passaro, N.; Garbuglia, A. R.; Capobianchi, M. R.; Crescenzi, M.; Valiente, G.; Pesole, G.

In: Bioinformatics, Vol. 33, No. 11, 01.06.2017, p. 1730-1732.

Research output: Contribution to journalArticle

Fosso, B. ; Santamaria, M. ; D'Antonio, M. ; Lovero, D. ; Corrado, G. ; Vizza, E. ; Passaro, N. ; Garbuglia, A. R. ; Capobianchi, M. R. ; Crescenzi, M. ; Valiente, G. ; Pesole, G. / MetaShot : An accurate workflow for taxon classification of host-associated microbiome from shotgun metagenomic data. In: Bioinformatics. 2017 ; Vol. 33, No. 11. pp. 1730-1732.
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