Assemblytics

Assemblytics detects and analyzes genomic variants by comparing de novo genome assemblies to reference genomes and employs an anchor filtering method to improve robustness in repetitive regions.

Key Features:

• Alignment-based detection: Detects variants by aligning de novo genome assemblies to reference genomes.
• Anchor filtering approach: Uses an anchor filtering technique to mitigate issues caused by repetitive elements and reduce spurious variant calls.
• Variant classification: Identifies six distinct classes of variants based on their alignment signatures.
• Application flexibility: Supports comparisons of aberrant genomes such as human cancers to reference genomes and identification of genetic differences between related species.
• Visualizations: Provides multiple visualizations to explore the genomic distribution and characteristics of detected variants.

Scientific Applications:

• Cancer genomics: Comparison of cancer genomes to reference genomes to identify mutations and structural variations relevant to oncogenesis and disease progression.
• Comparative genomics: Identification of genetic differences between related species to inform evolutionary and functional analyses.
• Genome annotation and evolutionary studies: Classification of variants and variant distributions to support genome annotation and studies of genomic evolution.

Methodology:

Align de novo assembled genomes to reference genomes, apply anchor filtering to enhance detection in repetitive regions, and identify six variant classes characterized by distinct alignment signatures.