Karyon

Karyon diagnoses and characterizes non-standard genome architectures such as high heterozygosity, polyploidy, and aneuploidy from raw sequencing data using de novo assembly and analytical plots.

Key Features:

• Implementation: Python-based toolkit that processes raw sequencing data and assembly outputs.
• Input data: Uses raw sequencing reads and original sequencing libraries for assembly and downstream analyses.
• De novo assembly: Includes automated pipelines for de novo genome assembly.
• Heterozygosity reduction (redundans): Reduces heterozygosity during assembly using redundans (Pryszcz & Gabaldón 2016).
• Mapping-based analysis: Maps original sequencing libraries against the reduced assembly to analyze the distribution of heterozygous regions.
• Variant calling: Provides automated variant calling pipelines as part of the analysis workflow.
• Plot generation: Generates diagnostic plots that visualize heterozygosity and other non-canonical genomic traits.
• Empirical evaluation: Applied to 35 highly fragmented public assemblies from 19 species of Mucorales (Fungi), with ~17% showing signs of unusual genomic configurations.

Scientific Applications:

• Diagnosis of non-standard genomes: Detects and characterizes high heterozygosity, polyploidy, aneuploidy, and other non-canonical architectures from sequencing data.
• Assembly assessment: Evaluates fragmented assemblies to reveal hidden complexity that may affect assembly quality and interpretation.
• Fungal genomics: Identifies unusual genomic configurations in fungal datasets, exemplified by analyses of Mucorales species.

Methodology:

Reduces heterozygosity during assembly using redundans; maps original sequencing libraries to the reduced assembly to analyze heterozygous region distribution; runs automated de novo assembly and variant calling pipelines and generates diagnostic plots.