title: Orione, a web-based framework for NGS analysis in microbiology.
abstract: End-to-end next-generation sequencing microbiology data analysis requires a diversity of tools covering bacterial resequencing, de novo assembly, scaffolding, bacterial RNA-Seq, gene annotation and metagenomics. However, the construction of computational pipelines that use different software packages is difficult owing to a lack of interoperability, reproducibility and transparency. To overcome these limitations we present Orione, a Galaxy-based framework consisting of publicly available research software and specifically designed pipelines to build complex, reproducible workflows for next-generation sequencing microbiology data analysis. Enabling microbiology researchers to conduct their own custom analysis and data manipulation without software installation or programming, Orione provides new opportunities for data-intensive computational analyses in microbiology and metagenomics.
  
  
  METHODS
  Orione is available online at http://orione.crs4.it.
authors.affiliation: CRS4, Science and Technology Park Polaris, Piscina Manna, 09010 Pula (CA), Italy.
authors.forename: Gianmauro
authors.initials: G
authors.lastname: Cuccuru
authors.affiliation: CRS4, Science and Technology Park Polaris, Piscina Manna, 09010 Pula (CA), Italy.
authors.forename: Massimiliano
authors.initials: M
authors.lastname: Orsini
authors.affiliation: CRS4, Science and Technology Park Polaris, Piscina Manna, 09010 Pula (CA), Italy.
authors.forename: Andrea
authors.initials: A
authors.lastname: Pinna
authors.affiliation: CRS4, Science and Technology Park Polaris, Piscina Manna, 09010 Pula (CA), Italy.
authors.forename: Andrea
authors.initials: A
authors.lastname: Sbardellati
authors.affiliation: CRS4, Science and Technology Park Polaris, Piscina Manna, 09010 Pula (CA), Italy.
authors.forename: Nicola
authors.initials: N
authors.lastname: Soranzo
authors.affiliation: CRS4, Science and Technology Park Polaris, Piscina Manna, 09010 Pula (CA), Italy.
authors.forename: Antonella
authors.initials: A
authors.lastname: Travaglione
authors.affiliation: CRS4, Science and Technology Park Polaris, Piscina Manna, 09010 Pula (CA), Italy.
authors.forename: Paolo
authors.initials: P
authors.lastname: Uva
authors.affiliation: CRS4, Science and Technology Park Polaris, Piscina Manna, 09010 Pula (CA), Italy.
authors.forename: Gianluigi
authors.initials: G
authors.lastname: Zanetti
authors.affiliation: CRS4, Science and Technology Park Polaris, Piscina Manna, 09010 Pula (CA), Italy.
authors.forename: Giorgio
authors.initials: G
authors.lastname: Fotia
mesh_terms: D059014:High-Throughput Nucleotide Sequencing; D020407:Internet; D056186:Metagenomics; D008828:Microbiological Techniques; D015203:Reproducibility of Results; D012984:Software