GenoMycAnalyzer

GenoMycAnalyzer analyzes Mycobacterium whole-genome sequencing (WGS) data to identify species, predict MTBC lineages and spoligotypes, and predict genotypic drug susceptibility for clinical and epidemiological use.

Key Features:

• Species identification and lineage/spoligotype prediction: Uses Kraken2 for taxonomic classification with reported species identification accuracy of 98.8% and perfect predictions for MTBC lineages and spoligotypes.
• Drug resistance determination (gDST): Predicts genotypic susceptibility for 15 antituberculosis drugs based on the WHO mutational catalogue, reporting sensitivities such as rifampicin 95.9% and levofloxacin 98.2% and specificity examples such as amikacin 98.7%.
• Variant calling and annotation: Performs comprehensive variant calling and annotation to characterize mutations associated with resistance.
• Detection of large deletions: Integrates large-deletion detection in resistance-conferring genes to improve genotypic resistance prediction.
• Data visualization: Provides visualization capabilities to aid interpretation of WGS-derived results.

Scientific Applications:

• Clinical management of tuberculosis: Supports informed treatment decisions by predicting species, MTBC lineage, spoligotype, and drug resistance from WGS data.
• Epidemiological investigations: Enables lineage and spoligotype assignment for molecular epidemiology and outbreak analysis.
• Interpretation of WGS data in diagnostics: Streamlines interpretation of whole-genome sequencing results for clinical diagnostic workflows.
• Public health surveillance: Supports surveillance activities by providing standardized species, lineage, and resistance information from genomic data.

Methodology:

Processes WGS data using Kraken2 for taxonomic classification, performs variant calling and annotation, predicts genotypic drug susceptibility using the WHO mutational catalogue, detects large deletions in resistance genes, and generates MTBC lineage and spoligotype predictions.