findGSEP

findGSEP estimates genome size of polyploid species using k-mer frequencies by iteratively fitting curves to disentangle genomic regions and infer both full polyploid and average haploid genome size.

Key Features:

• Iterative curve fitting: Disentangles up to p normal distributions by analyzing k-mer frequencies in whole genome sequencing data.
• Ploidy flexibility: Handles any level of ploidy p, including high ploidy levels such as octoploids.
• Genome size inference: Computes sizes of genomic regions related to 1 to p homologous chromosomes and infers full polyploid and average haploid genome size.
• Parallel processing: Implemented as an R package supporting parallel processing of multiple samples.

Scientific Applications:

• Polyploid genome size estimation: Estimates genome size for polyploid species where ploidy p is greater than 2, addressing a long-standing challenge in genome sequencing project design.
• Sequencing project design: Provides fundamental genome size parameters needed for designing genome sequencing and analysis projects.
• Validation across species: Demonstrated on simulated and real genomic sequencing data of various species including octoploids, showing improved accuracy over other well-known tools.

Methodology:

findGSEP uses iterative curve fitting of k-mer frequencies. It first disentangles up to p normal distributions by analyzing k-mer frequencies in whole genome sequencing data. It then computes the sizes of genomic regions related to 1 to p homologous chromosomes using each respective curve fitting, from which it infers the full polyploid and average haploid genome size.