icHET

icHET visualizes genome-wide cytoplasmic heteroplasmy from short-read sequencing data to support comparative analysis across multiple samples using organellar (mitochondrial, plastid) and nuclear reference genomes.

Key Features:

• Heteroplasmy visualization: Generates visual representations of heteroplasmic sites across genomes derived from short-read sequencing data.
• Genome-wide analysis: Processes heteroplasmy signals across entire organellar and nuclear genomes.
• Cross-sample comparison: Supports analysis and comparison of heteroplasmic variation across multiple samples.
• Organellar and nuclear integration: Integrates short reads with organellar (mitochondrial, plastid) and nuclear reference genomes for joint analysis.
• Taxonomic flexibility: Applicable to diverse organisms provided organellar and nuclear reference genomes are available.

Scientific Applications:

• Organellar heteroplasmy studies: Analysis of heteroplasmy in mitochondria and plastids across samples.
• Comparative population genetics: Comparative assessment of heteroplasmic variation within and between populations or species.
• Evolutionary biology: Investigation of heteroplasmy patterns relevant to evolutionary processes.
• Disease-associated heteroplasmy research: Examination of heteroplasmic variants that may be implicated in disease contexts.

Methodology:

Processes short-read sequencing data from multiple samples and integrates reads with organellar and nuclear reference genomes to identify and visualize heteroplasmic sites genome-wide.