MetaGeneSense

MetaGeneSense detects, characterizes, and classifies pathogens from high-throughput sequencing (HTS/NGS) data to support metagenomic and public-health analyses.

Key Features:

• Galaxy Workflow Integration: Facilitates organization, exploration, and aggregation of sample-specific sequences from millions of genomic reads and enables determination of relative abundance and association with closely related organisms or pathogens.
• API-Based Interaction (BioBlend): Provides API-based access to Galaxy core functionalities via the BioBlend library.
• Processing Steps: Supports loading, indexing, mapping, assembly, and database searches of HTS/NGS data.
• Compute and Storage Integration: Integrates with storage and grid computing resources to handle large-scale sequencing data processing.
• Metadata Management (LIMS): Stores metadata for samples, runs, and workflow results in a Laboratory Information Management System (LIMS).
• Exploratory Tools Integration (Krona): Integrates Krona for taxonomic classification visualization.
• Platform Architecture (Django): Employs a Django-based framework to link input data and metadata with Galaxy, storage, and compute resources.

Scientific Applications:

• Emerging pathogen detection: Identification and characterization of emerging infectious agents from complex biological samples using HTS/NGS data.
• Epidemiological studies: Analysis of metagenomic data to determine relative abundance and taxonomic associations relevant to population-level studies.
• Outbreak investigations: Rapid aggregation and classification of sequencing reads to support investigation and source attribution of outbreaks.
• Routine pathogen surveillance: Large-scale processing and archival of sequencing runs and metadata to support ongoing surveillance programs.

Methodology:

Execution of Galaxy workflows via the BioBlend API to process HTS/NGS reads with loading, indexing, mapping, assembly, and database searches; metadata are recorded in a LIMS and Krona is used for taxonomic visualization.