NEXTmicro: An integrated solution for the analysis and monitoring of outbreaks
NEXTmicro started as a project that was carried out during 2012 and 2013, funded in part by the Spanish CDTI (Centro para el Desarrollo Tecnológico Industrial). Thanks to the next generation sequencing technologies probably during the next years the whole genome sequencing will be a standard for the management of outbreaks from hospital environments and health protection agencies. The goal of NEXTmicro was to create a platform to manage all the data related to NGS sequencing, gene annotation and comparative genomics analysis in the context of an outbreak.
NEXTmicro includes our BG7 annotation system (See publication about BG7 in PLOS ONE), Cloud Computing pipelines needed for handling the vast amount of data generated, as well as other services to facilitate the access and interpretation of the results for the staff at the hospital or health care setting where the outbreak takes place.
With this service you will get a continuous support from Era7, which offers solutions to all the steps from the design of the project to the storage of the data:
- Sample reception and management
- Design of the sequencing strategy that best fits each case
- Sequencing. Using the most appropriate technology depending on the needs that the outbreak demands
- Quick Assembly and functional annotation based on BG7
- Study of pathogenicity, virulence and antibiotic resistance genes
- Complete comparative genomics analysis, with continuously updated pipelines that include the standard core genome SNP-based phylogenetic analysis and also whole genome comparisons that give insight on functional differences in the isolates.
- Design of tools for the molecular diagnostics of the causative agent of epidemics
- Data Storage and management