title: MetaShot: an accurate workflow for taxon classification of host-associated microbiome from shotgun metagenomic data.
abstract: CONCLUSIONS
  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.
  
  
  METHODS
  https://github.com/bfosso/MetaShot.
  
  
  BACKGROUND
  graziano.pesole@uniba.it.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Institute of Biomembranes and Bioenergetics, Consiglio Nazionale delle Ricerche, Bari, Italy.
authors.forename: B
authors.initials: B
authors.lastname: Fosso
authors.affiliation: Institute of Biomembranes and Bioenergetics, Consiglio Nazionale delle Ricerche, Bari, Italy.
authors.forename: M
authors.initials: M
authors.lastname: Santamaria
authors.affiliation: CINECA, Rome, Italy.
authors.forename: M
authors.initials: M
authors.lastname: D'Antonio
authors.affiliation: Institute of Biomembranes and Bioenergetics, Consiglio Nazionale delle Ricerche, Bari, Italy.
authors.forename: D
authors.initials: D
authors.lastname: Lovero
authors.affiliation: Department of Oncological Surgery, Gynecologic Oncology Unit, "Regina Elena" National Cancer Institute, Rome, Italy.
authors.forename: G
authors.initials: G
authors.lastname: Corrado
authors.affiliation: Department of Oncological Surgery, Gynecologic Oncology Unit, "Regina Elena" National Cancer Institute, Rome, Italy.
authors.forename: E
authors.initials: E
authors.lastname: Vizza
authors.affiliation: Department of Cell Biology and Neurosciences, Italian National Institute of Health, Rome, Italy.
authors.forename: N
authors.initials: N
authors.lastname: Passaro
authors.affiliation: Lazzaro Spallanzani National Institute for Infectious Diseases, Rome, Italy.
authors.forename: A R
authors.initials: AR
authors.lastname: Garbuglia
authors.affiliation: Lazzaro Spallanzani National Institute for Infectious Diseases, Rome, Italy.
authors.forename: M R
authors.initials: MR
authors.lastname: Capobianchi
authors.affiliation: Department of Cell Biology and Neurosciences, Italian National Institute of Health, Rome, Italy.
authors.forename: M
authors.initials: M
authors.lastname: Crescenzi
authors.affiliation: Algorithms, Bioinformatics, Complexity and Formal Methods Research Group, Technical University of Catalonia, Barcelona, Spain.
authors.forename: G
authors.initials: G
authors.lastname: Valiente
authors.affiliation: Institute of Biomembranes and Bioenergetics, Consiglio Nazionale delle Ricerche, Bari, Italy.|Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari "A. Moro", Bari, Italy.
authors.forename: G
authors.initials: G
authors.lastname: Pesole
mesh_terms: D000465:Algorithms; D001419:Bacteria / Q000145:classification / Q000235:genetics; D005658:Fungi / Q000145:classification / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D056186:Metagenomics / Q000379:methods*; D064307:Microbiota / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software; D014780:Viruses / Q000145:classification / Q000235:genetics; D057188:Workflow