GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes

An important assessment prior to genome assembly and related analyses is genome profiling, where the k-mer frequencies within raw sequencing reads are analyzed to estimate major genome characteristics such as size, heterozygosity, and repetitiveness. Here we introduce GenomeScope 2.0 (https://github.com/tbenavi1/genomescope2.0), which applies combinatorial theory to establish a detailed mathematical model of how k-mer frequencies are distributed in heterozygous and polyploid genomes. We describe and evaluate a practical implementation of the polyploid-aware mixture model that quickly and accurately infers genome properties across thousands of simulated and several real datasets spanning a broad range of…

• NS
  National Science Foundation

  Awards: 1732253, DBI-1350041, R01-HG006677, 1350041, IOS-1732253
• MA
  Maryland Advanced Research Computing Center
• NI
  National Institutes of Health

  Awards: R01-HG006677, HG006677