GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes
By T. Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz. Nature Communications, 2020
2,300 citations recorded by the source corpus.
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/smudgeplot) to visualize and estimate 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 the extreme case of octoploid Fragaria × ananassa. Prior to genome assembly, the raw sequencing reads must be analyzed for assessment of major genome characteristics such as genome size, heterozygosity, and repetitiveness. For this purpose, the authors introduce GenomeScope 2.0, an extension of GenomeScope for polyploid genomes, and Smudgeplot, which can estimate a genome’s ploidy.
Subfields: Plant Science
View Paper: https://www.semanticscholar.org/paper/659ea5c35c244a35e48d12eefcd5ea113fbc8638
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Citations in the corpus
- JCVI: A versatile toolkit for comparative genomics analysis (2024, methodology): “The raw sequencing data can often be used to derive the basic statistics of a genome through the analysis of K ‐ mer spectra [31].”
- A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas (2020, positive): “0 (GenomeScope, RRID:SCR 017014) [40], based on the quality-filtered Illumina reads.”
- Significantly improving the quality of genome assemblies through curation (2020, neutral): “whether the assembly contains all the relevant kmers present in the reads) and the ploidy of the genome [14].”