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- W4303519741 abstract "Abstract Background Recent technological developments have made genome sequencing and assembly highly accessible and widely used. However, the presence in sequenced organisms of certain genomic features such as high heterozygosity, polyploidy, aneuploidy, heterokaryosis, or extreme compositional biases can challenge current standard assembly procedures and result in highly fragmented assemblies. Hence, we hypothesized that genome databases must contain a nonnegligible fraction of low-quality assemblies that result from such type of intrinsic genomic factors. Findings Here we present Karyon, a Python-based toolkit that uses raw sequencing data and de novo genome assembly to assess several parameters and generate informative plots to assist in the identification of nonchanonical genomic traits. Karyon includes automated de novo genome assembly and variant calling pipelines. We tested Karyon by diagnosing 35 highly fragmented publicly available assemblies from 19 different Mucorales (Fungi) species. Conclusions Our results show that 10 (28.57%) of the assemblies presented signs of unusual genomic configurations, suggesting that these are common, at least for some lineages within the Fungi." @default.
- W4303519741 created "2022-10-08" @default.
- W4303519741 creator A5000264042 @default.
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- W4303519741 date "2022-01-01" @default.
- W4303519741 modified "2023-10-18" @default.
- W4303519741 title "Karyon: a computational framework for the diagnosis of hybrids, aneuploids, and other nonstandard architectures in genome assemblies" @default.
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- W4303519741 doi "https://doi.org/10.1093/gigascience/giac088" @default.
- W4303519741 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/36205401" @default.
- W4303519741 hasPublicationYear "2022" @default.
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