draft at bioRxiv: Genes ruler for genomes, Gnodes, measures assembly accuracy

[Don Gilbert]

Dear all,

Gnodes public draft paper is available since last month.  Anyone who tries this new Evigene package will find me helpful in getting it to work for you, and help understanding its results.  I am still working on Gnodes, with some improvements coming soon.

-- Don Gilbert

Abstract: Gnodes is a Genome Depth Estimator for animal and plant genomes, also a genome size estimator. It calculates genome sizes based on DNA coverage of assemblies, using unique, conserved gene spans for its standard depth. Results of this tool match the independent measures from flow cytometry of genome size quite well in tests with plants and animals. Tests on a range of model and non-model animal and plant genome assemblies give reliable and accurate results, in contrast to less reliable K-mer histogram methods. The problem of half-sized assemblies of duplication-rich Daphnia is addressed. A 20-year old Arabidopsis genome discrepancy is resolved in favor of 157Mb as measured with flow-cytometry. Not all genome DNA samples contain a genome, examples and reasons for this are discussed. The T2T completed human genome assembly of 2022 is complete by Gnodes measures, with about 5% uncertainty. With full genome DNA, Gnodes measures within 10%, usually within 5%, of flow cytometry, indicating they are both measuring the same content. Public URL: http://eugenes.org/EvidentialGene/other/gnodes/

This doc at bioRxiv with doi: 10.1101/2022.05.13.491861

and here with all supplemental data (new Arabidopsis assembly, etc)