ploidyNGS

ploidyNGS analyzes short-read next-generation sequencing (NGS) data to detect and visualize genome ploidy levels by assessing copy number variation.

Key Features:

• Model-Free Approach: Operates without predefined models, enabling data-driven analysis of ploidy from sequencing data.
• Implementation: Implemented in Python and R.
• Short-Read NGS Support: Uses short reads generated by next-generation sequencing (NGS) technologies.
• Copy Number Variation Assessment: Assesses genome-wide copy number variations indicative of different ploidy levels.
• Visual Data Representation: Produces visual representations for exploration and interpretation of ploidy levels.
• Demonstrated Data: Validated on both simulated and real NGS data from Saccharomyces cerevisiae.

Scientific Applications:

• Ploidy Determination: Determination of ploidy levels in newly sequenced genomes using short-read NGS data.
• Polyploidy and Genome Duplication Studies: Investigation of polyploid organisms and genome duplication events.
• Validation and Benchmarking: Method validation and benchmarking using simulated datasets and Saccharomyces cerevisiae NGS data.

Methodology:

Processes short-read NGS data to assess genome-wide copy number variations and generates visual representations to identify ploidy states.