chewie-NS

chewie-NS provides a centralized nomenclature server for genome-based gene-by-gene typing schemas, enabling standardized sharing and comparison of allelic data and schemas.

Key Features:

• Common Nomenclature Maintenance: Maintains consistent allele and schema nomenclature across studies for gene-by-gene typing.
• Data Sharing with Confidentiality: Balances local analyses and a public allelic repository to enable comparisons while preserving data confidentiality.
• Private Instances Deployment: Supports deployment of private chewie-NS instances to host restricted-access nomenclature servers.
• Interactive Data Exploration: Provides charts and tables that report statistics on schemas and loci.
• Schema Management: Enables sharing of typing schemas and retrieval of information required to run schemas locally and to access alleles at specific loci.
• Integration with chewBBACA Suite: Integrates with the chewBBACA suite to upload, download, and synchronize schemas between local installations and the server via the command-line version of chewBBACA.
• REST API Support: Exposes a REST API to link chewie-NS and chewBBACA and to allow other interfaces or pipelines to interact with chewie-NS databases.

Scientific Applications:

• Gene-by-gene typing standardization: Standardizes allele nomenclature for genome-based gene-by-gene typing schemas.
• Comparative allelic analysis: Compares allelic profiles and schemas across studies and repositories to improve reproducibility and comparability.
• High-throughput typing pipelines: Supports high-throughput genome-based typing pipelines via schema synchronization and programmatic access.

Methodology:

Schemas are uploaded, downloaded, and synchronized via the command-line version of chewBBACA; a REST API enables programmatic interaction with chewie-NS databases; the server generates charts and tables reporting statistics on schemas and loci.