Gnodes/Genome Depth Estimator paper #3
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Don Gilbert
Oct 24, 2023, 2:24:32 PM10/24/23
to EvidentialGene
Dear genome/gene biologists and informaticians,
A Gnodes#3 draft document is here, not quite finished, but main contents are in. I value any comments you may have on this, which I hope will be understandable and useful to a range of genome biologists and informaticians.
http://arthropods.eugenes.org/EvidentialGene/other/gnodes/gnodesdoc/
gnodes_doc3d.pdf
"Measure of major contents in animal and plant genomes, using Gnodes, finds under-assemblies of model plant, Daphnia, fire ant and others."
There are many details not yet included in Gnodes#3 doc. If you have thoughts on what needs to be added, or what parts are too verbose and can be shortened, please let me know.
There are some new genome assemblies, in the gnodesdoc/gnodes_newasm23/ subfolder. The one of most general interest would be arabidopsis23chrs/ which contain a measurably complete chromosome set for this model plant.
There is a yet-to-be written Gnodes#2 doc; I have its many tables, but text tying it together isn't ready. This #2 has less interesting, gory details of "Measuring DNA contents of animal and plant genomes with Gnodes, the long and short of it." I.e., measuring genomes with DNA long-reads, short-reads, effects of various software, biological and methodological things).
Gnodes#1 doc is there as gnodes_doc2g.pdf
"Genes ruler for genomes, Gnodes, measures assembly accuracy in animals and plants."
which introduces and covers the workings of this tool. It remains generally accurate with caveats this is a complex area, where details matter. E.g. K-mer methods to estimate genome sizes miss much of the higher-order repeats of genomes, that Gnodes measures, probably due to having a bad default value that cuts out those HORs.
A Gnodes#3 draft document is here, not quite finished, but main contents are in. I value any comments you may have on this, which I hope will be understandable and useful to a range of genome biologists and informaticians.
http://arthropods.eugenes.org/EvidentialGene/other/gnodes/gnodesdoc/
gnodes_doc3d.pdf
"Measure of major contents in animal and plant genomes, using Gnodes, finds under-assemblies of model plant, Daphnia, fire ant and others."
There are many details not yet included in Gnodes#3 doc. If you have thoughts on what needs to be added, or what parts are too verbose and can be shortened, please let me know.
There are some new genome assemblies, in the gnodesdoc/gnodes_newasm23/ subfolder. The one of most general interest would be arabidopsis23chrs/ which contain a measurably complete chromosome set for this model plant.
There is a yet-to-be written Gnodes#2 doc; I have its many tables, but text tying it together isn't ready. This #2 has less interesting, gory details of "Measuring DNA contents of animal and plant genomes with Gnodes, the long and short of it." I.e., measuring genomes with DNA long-reads, short-reads, effects of various software, biological and methodological things).
Gnodes#1 doc is there as gnodes_doc2g.pdf
"Genes ruler for genomes, Gnodes, measures assembly accuracy in animals and plants."
which introduces and covers the workings of this tool. It remains generally accurate with caveats this is a complex area, where details matter. E.g. K-mer methods to estimate genome sizes miss much of the higher-order repeats of genomes, that Gnodes measures, probably due to having a bad default value that cuts out those HORs.
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