The DOI matches its Crossref record; 39 of the 39 references it cites were found in a registry or an index.
GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes
Open accessAbstract
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 .
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BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
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Self-citationGenomeScope: fast reference-free genome profiling from short reads
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Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita
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Metadata
- Authors
- Ranallo-Benavidez, T. R., Jaron, K. S., & Schatz, M. C.
- Venue
- Nature Communications
- Published
- 2020-03-18
- Volume
- 11
- Issue
- 1
- Pages
- 1432-1432
- ISSN
- 2041-1723 (ISSN-L)
- OpenAlex
- W3012094285
- Cited by
- 2,759
- References
- 39
- FWCI
- 40.11
- Type
- journal article
- Language
- en
- Open access
- gold
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