Genes ruler for genomes, Gnodes, measures assembly accuracy in animals and plants.
by Don Gilbert, gilbertd@indiana.edu, 2022 May.

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

gnodes#3 ------------------------------------------------------------------o

Measure of major contents in animal and plant genomes, using Gnodes, 
finds under-assemblies of Daphnia, fire ant, flies, lice and model plant.
by Don Gilbert, gilbertd@indiana.edu, 2023

Abstract to be written
gnodes_doc3d.pdf is new work and content, not an update to gnodes_doc2g.pdf but extension.