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Bioinformatics. 2014 Jul 1;30(13):1928-9. doi: 10.1093/bioinformatics/btu135. Epub 2014 Mar 10.

Orione, a web-based framework for NGS analysis in microbiology.

Author information

1
CRS4, Science and Technology Park Polaris, Piscina Manna, 09010 Pula (CA), Italy.

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.

AVAILABILITY AND IMPLEMENTATION:

Orione is available online at http://orione.crs4.it.

PMID:
24618473
PMCID:
PMC4071203
DOI:
10.1093/bioinformatics/btu135
[Indexed for MEDLINE]
Free PMC Article

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