Supporting data for "Karyon: a computational framework for the diagnosis of hybrids, aneuploids, and other non-standard architectures in genome assemblies"

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 non-negligible fraction of low-quality assemblies that result from such type of intrinsic genomic factors. Here we present Karyon, a Python-based toolkit that uses raw sequencing data and <i>de novo</i> genome assembly to assess several parameters and generate informative plots to assist in the identification of non-chanonical genomic traits. Karyon includes automated <i>de novo</i> genome assembly and variant calling pipelines. We tested Karyon by diagnosing 35 highly fragmented publicly available assemblies from 19 different Mucorales (Fungi) species. 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.