GRACy

GRACy reconstructs and annotates human cytomegalovirus (HCMV) genomes from Illumina sequencing data to support genotyping, variant detection, and downstream genomic analyses.

Key Features:

• Read Quality Filtering: Automated modules perform read quality filtering to select high-quality Illumina sequencing reads for reliable downstream analysis.
• Genotyping: Facilitates accurate genotyping of HCMV strains to characterize viral diversity.
• De Novo Assembly: Supports de novo genome assembly from raw sequence data to reconstruct complete or near-complete HCMV genomes without a reference.
• Variant Detection: Provides variant analysis capabilities to identify mutations of potential clinical significance.
• Genome Annotation: Automates annotation of genomic features and links them to functional information.
• Data Submission: Implements pathways for submitting sequence data and annotations to public databases.

Scientific Applications:

• Viral evolution: Enables comparative analyses to investigate HCMV evolutionary dynamics.
• Pathogenesis studies: Supports genomic investigations into determinants of HCMV pathogenesis.
• Resistance mechanism analysis: Facilitates detection and study of mutations associated with antiviral resistance.
• Clinical and diagnostic genomics: Provides genomic data and annotations to inform clinical research and diagnostic investigations.

Methodology:

Performs automated read quality filtering, HCMV genotyping, de novo assembly, variant detection, genome annotation, and data submission workflows and is implemented in Python; it has been tested on simulated and experimental datasets.