Nebula Genomics (30x Whole Genome Sequencing)

Jovialis: I went to Admixture Studio and ran the Dodecad 12B calculators using my 4 files

Ancestry+23_ME: Genotype Coverage = 92.76%
Ancestry: Genotype Coverage = 91.19%
NATGENO: Genotype Coverage = 48.58%
23_ME: Genotype Coverage = 28.39%

So my results, and yours suggest to me, that even with only for example 28.39% Genome coverage for my 23_ME, the Dodecad 12B calculator does a really good job of estimating ethnicity accurately. Still it does show a clear difference in coverage.

Regards, PT
 
the older and newer WGSE outputs slightly different combined results, ... if the ancient output .zip file is below or around 5mb WGSE-3 will delete it, if you are fast enough, you can copy and paste it into another directory, though if the output .zip is very small it won't show up at all.

example:

... VK537 coverage - WGSE old vs WGSE-3
pzhfdBO.gif


(my combined: Ancestry, 23v4, 23v5, LivDNA, NatGeo)

jEQYpSv.gif


Code:
VK537_WG_old_CombinedKit_Dod_K12b,5.21,0.93,4.78,0.00,26.19,16.86,0.95,0.70,11.33,0.35,31.41,1.30
VK537_WG_3_CombinedKit_Dod_K12b,5.46,0.95,4.75,0.00,25.91,17.01,0.81,1.01,11.42,0.68,30.55,1.47
 
^^Indeed, I think because the new WGSExtract has a Human Genome Reference specifically tailored for aDNA. I saw it when I clicked on the install batch file.

OMG, it would be insane to do all those BAM files all over again! I can't even fathom it.
 
^^Indeed, I think because the new WGSExtract has a Human Genome Reference specifically tailored for aDNA. I saw it when I clicked on the install batch file.

OMG, it would be insane to do all those BAM files all over again! I can't even fathom it.

It’s all good :) the difference is minimal and the top matches are usually the same.
 
Well guys thank you.

I knew FTDNA had to be low due to se no reads with services in the past. But 40%?! That is beyond an F- ...

Really will try to snipe a sale on this.
 
Jovialis: I went to Admixture Studio and ran the Dodecad 12B calculators using my 4 files

Ancestry+23_ME: Genotype Coverage = 92.76%
Ancestry: Genotype Coverage = 91.19%
NATGENO: Genotype Coverage = 48.58%
23_ME: Genotype Coverage = 28.39%

So my results, and yours suggest to me, that even with only for example 28.39% Genome coverage for my 23_ME, the Dodecad 12B calculator does a really good job of estimating ethnicity accurately. Still it does show a clear difference in coverage.

Regards, PT

You could combine Nat Geno 2.0 with the other two in DNA kit studio, to see if it can give you a higher coverage.
 
You could combine Nat Geno 2.0 with the other two in DNA kit studio, to see if it can give you a higher coverage.

Jovialis: Thanks, DNA Kit Studio, is that free or need to be purchased. I was able to combine the other 2 with GEDMATCH for a Combined GEDMATCH Kit and a colleague of mine (Data analytics) used Alteryx to combine the two into a file I could use for Admixture studio. NAT GENO (I don't have the Helix version) is in a different format but might be able to get it into a format that can be combined with other two.
 
Jovialis: Thanks, DNA Kit Studio, is that free or need to be purchased. I was able to combine the other 2 with GEDMATCH for a Combined GEDMATCH Kit and a colleague of mine (Data analytics) used Alteryx to combine the two into a file I could use for Admixture studio. NAT GENO (I don't have the Helix version) is in a different format but might be able to get it into a format that can be combined with other two.

Yep, DNA Kit studio is a free software.
 
Jovialis: Ok, thanks
 
Distance to:Jovialis_Nebula
0.49608467Jovialis_Superkit

Could you puy in the calc all your kits just like that so we can see the distances betwen them?
 
Could you puy in the calc all your kits just like that so we can see the distances betwen them?

This is Dodecad Globe 13:

Distance to:Jovialis:Nebula
0.47455242Jovialis:AncestryDNA
0.49608467Jovialis:Superkit
1.18004237Jovialis:FTDNA
1.26751726Jovialis:Nat_Geo_Helix_2.0
2.21262288Jovialis:Living_DNA
2.36122849Jovialis:23andme_V5


This is Dodecad K12b:

Distance to:Jovialis:Nebula
0.59531504Jovialis:Superkit
0.77440300Jovialis:AncestryDNA
1.69289693Jovialis:FTDNA
1.75570499Jovialis:Nat_Geo_Helix_2.0
3.59815230Jovialis:Living_DNA
3.65116420Jovialis:23andme_V5


The distance is a lot closer than the PCA would lead me to believe.
 
This is Dodecad Globe 13:

Distance to:Jovialis:Nebula
0.47455242Jovialis:AncestryDNA
0.49608467Jovialis:Superkit
1.18004237Jovialis:FTDNA
1.26751726Jovialis:Nat_Geo_Helix_2.0
2.21262288Jovialis:Living_DNA
2.36122849Jovialis:23andme_V5

This is Dodecad K12b:

Distance to:Jovialis:Nebula
0.59531504Jovialis:Superkit
0.77440300Jovialis:AncestryDNA
1.69289693Jovialis:FTDNA
1.75570499Jovialis:Nat_Geo_Helix_2.0
3.59815230Jovialis:Living_DNA
3.65116420Jovialis:23andme_V5

The distance is a lot closer than the PCA would lead me to believe.

Also interesting is that for Globe 13, the ancestry raw data is slightly closer to the Nebula sample than the superkit, despite having lower coverage. Albeit, infinitesimal, it seems the slightly higher coverage for the superkit skewed it a tiny bit. But once the rest of the coverage was met by the Nebula raw data, it pulled it back to the appropriate position.
 
Ancestry you meant I am sure.

And yes that is quite interesting. Just a coincidence surely. But really puts Ancestry in a good light.
 
FilenameCalculatorGenotype ratio
Merged kits.txtDodecad K12b97,61%

Vahaduo Dodecad K12b updated

Distance toDk12ComboD
5.49689913Portuguese
5.75458078Spanish_Canarias
6.58738188Spanish_Castilla-Leon
6.96282988Spanish_Galicia
7.28287031Spanish_Valencia
7.37196039Spanish_Andalusia
7.83413684Spanish_Baleares
8.22455470Spanish_Asturias
8.50034705Spanish_Catalonia
8.83516270Spanish_Aragon
9.50052104Spanish_Cantabria
10.77207501Italian_Aosta_Valley
11.53501192Spanish_La_Rioja
12.40179826Italian_Piedmont
12.41317496Swiss_Italian
12.79627289Italian_Lombardy
13.16973804Italian_Trentino
13.71645362Italian_Liguria
14.00724455Italian_Veneto
14.49210820Italian_Emilia
14.54362747French_Southwest
15.33367536Italian_Friuli_VG
15.88246203Italian_Tuscany
16.03369577French_Corsica
16.51399709French_Northeast

Target: Dk12ComboD
Distance: 4.3568% / 4.35682776

84.0Spanish_Canarias
16.0Spanish_Basque



 
At 30x/100bp there is a huge difference between the number of mutations reported on the Y chromosome compared to 30x/150bp as they promised. Thus at 100bp there are 6600 mutations and at 150bp there are 8310 mutations signaled in the vcf files. 25% higher at 150bp!

Yeah, it is unfortunate that I couldn't get the 150 bp, because they made the switch.
 
Hello, I am sorry if this is not the most appropriate thread for this.
I have been waiting for Nebula kit, now by the tracking number I see it is held by customs (EU country). It looks like they are going to ask for the receipt or something. I am not sure how to handle it as the kit it self is for free, right? How can I declare it value? I contacted Nebula but haven't got any reply for now. Thanks.
 
Hello, I am sorry if this is not the most appropriate thread for this.
I have been waiting for Nebula kit, now by the tracking number I see it is held by customs (EU country). It looks like they are going to ask for the receipt or something. I am not sure how to handle it as the kit it self is for free, right? How can I declare it value? I contacted Nebula but haven't got any reply for now. Thanks.

Took a few days for them to respond to my queries. If you don't hear back from them, you should try again.
 

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