GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes
GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes
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London: Nature Publishing Group UK
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English
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London: Nature Publishing Group UK
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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 sever...
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GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes
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TN_cdi_doaj_primary_oai_doaj_org_article_bb7ec6c178e2449d9f0806ad2d30d2eb
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https://devfeature-collection.sl.nsw.gov.au/record/TN_cdi_doaj_primary_oai_doaj_org_article_bb7ec6c178e2449d9f0806ad2d30d2eb
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ISSN
2041-1723
E-ISSN
2041-1723
DOI
10.1038/s41467-020-14998-3
