PT  - JOURNAL ARTICLE
AU  - Ranallo-Benavidez, T. Rhyker
AU  - Jaron, Kamil S.
AU  - Schatz, Michael C.
TI  - GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes
AID  - 10.1101/747568
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 747568
4099  - http://biorxiv.org/content/early/2019/08/26/747568.short
4100  - http://biorxiv.org/content/early/2019/08/26/747568.full
AB  - 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 genome 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, within seconds, accurately infers genome properties across thousands of simulated and eleven real datasets spanning a broad range of complexity. We also present a new method called Smudgeplots (https://github.com/KamilSJaron/smudgeplot) to visualize and infer the ploidy and genome structure of a genome by analyzing heterozygous k-mer pairs. We successfully apply the approach to systems of known variable ploidy levels in the Meloidogyne genus and also the extreme case of octoploid Fragaria x ananassa.