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

ABSTRACT: 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 complexity. We also present a method called Smudgeplot (https://github.com/KamilSJaron/

SUBMITTER: Ranallo-Benavidez TR 

PROVIDER: S-EPMC7080791 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature