Nebula Genomics (30x Whole Genome Sequencing)

[Jovialis]

I finally broke down, and decided to order myself a kit. I received 70% off for the Spring sale, but went with the lifetime member access, so it came out to $499 in total.

I will have a 30x WGS raw data file to utilize, which is the gold-standard of population genomics.

 

[Salento]

I finally broke down, and decided to order myself a kit. I received 70% off for the Spring sale, but went with the lifetime member access, so it came out to $499 in total.

I will have a 30x WGS raw data file to utilize, which is the gold-standard of population genomics.

Nice

... same price as the Helix Exome+ (whole exome sequencing), ...

... if it wasn’t for the lack of information regarding the Helix raw-data compatibility, I would have gotten it already.

 

[Jovialis]

^^For Nebula Genomics, I can download the VCF file, and convert it to a raw data file in a direct-to-consumer genomic format with DNAkit Studio.

 

[Salento]

^^For Nebula Genomics, I can download the VCF file, and convert it to a raw data file in a direct-to-consumer genomic format with DNAkit Studio.

Dna Land has the imputed VCF files, ... a while ago I downloaded and unzipped the “Human Genome Reference” and then I added it into the appropriate DNAkit studio folder, ...

I don't post the imputed Raw-Data results, and if I do, I'd say so.

When you get the Nebula Genomics results you could do an experiment and see the difference between normal and imputed VCF.

You could tell us about discrepancies and the validity of the imputed results

 

[Jovialis]

Dna Land has the imputed VCF files, ... a while ago I downloaded and unzipped the “Human Genome Reference” and then I added it into the appropriate DNAkit studio folder, ...
I don't post the imputed Raw-Data results, and if I do, I'd say so.
When you get the Nebula Genomics results you could do an experiment and see the difference between normal and imputed VCF.
You could tell us about discrepancies and the validity of the imputed results

I will also need to invest in an external hard drive, since the all of the files to download will be over 100 GBs. Though the VCF file is only about 300 MBs I believe.

 

[Jovialis]

Tomorrow I submit my sample back into the mail, and then it will be a waiting game from there. It should be 8-10 weeks turn around time, from when they receive the sample back. So hopefully by mid-June or early-July, my results should be ready.

 

[Jovialis]

I actually received a message 6 days ago, stating my sample has entered the quality control phase, and if it passes, it will be 6 weeks till my results are ready.

 

[torzio]

i got this part of an email yesterday

We ( Yfull ) have partnered with Nebula Genomics to give Nebula Genomics users access to the deep ancestry analysis provided by the YFull platform.

 

[lescoyi]

I finally broke down, and decided to order myself a kit. I received 70% off for the Spring sale, but went with the lifetime member access, so it came out to $499 in total.

I will have a 30x WGS raw data file to utilize, which is the gold-standard of population genomics.

Nice! I was comsidering Big Y but have beem advised that Nebula Genomics 30x is much better, so I will soon order with them. Partnered with YFull (where I have my mtDNA) is great, and they should have FTDNA on board too this year.

I'm not interested in the health analysis side, though Nebula says that you can order the monthly sub and can unsub anytime, retaining access to all the dna data presentation on the site, which will have a link to it on YFull.

 

[Jovialis]

They have indeed confirmed that my sample passed quality control; I e-mailed them on the day, asking them. They said the results should be ready by the first week of August.

Fingers-crossed.

 

[lescoyi]

Nebula failed to answer my question about FTDNA integration, just an "I'll pass on your question, please bear with us". So I went with Big Y. As said, I'm not interested in the health side of genomics. Maybe FTDNA will offer 100% sequencing in the future?

 

[Jovialis]

My Superkit which is a combination of 23andme V5, Ancestry DNA, Nat Geo Helix 2.0, FTDNA, and Living DNA, gives me a total of 1,224,690 SNPs.


There are about 4 to 5 million SNPs in the human genome. I am looking forward to obtaining my 30x WGS BAM file.

 

[Jovialis]

Finally got my results! I am in the process of downloading the large FASTQ and CRAM files. I also have VCF files too.

One problem though, when I run the VCF file in DNAkit studio, the results are all out of wack, and it only has about 52% genotype coverage.

So I decided to try to utilize the Human Genome Reference support linked here, to annotate the file:

https://dnagenics.com/dna-kit-studio/

but after downloading and unzipping the file, the results are still the same. Obviously I am doing something wrong here.

I know the file is good, because there are over 4 million SNPs, while my Superkit only have over 1 million. However, the Superkit has over 95% genotype coverage.

 

[Jovialis]

My alternative would be to convert the CRAM file to BAM, and run it through WGSextract. But that would cost me $20 to use EvE premium for a onetime use.

EDIT: Turns out you can't go from CRAM to BAM with EvE. Good thing I didn't buy it.

 

[Jovialis]

With the new WGSextract Beta 3, you can convert CRAM to BAM. I am in the process of doing that right now, which is taking a total of 1.5 hours. After that, I will run the BAM file as I normally would. Though I bet it will take quiet a bit due to the size of the file.

 

[Archetype0ne]

Hey Jov. Does this company offer health and nutrition services?
I bet with such deep coverage this must have a lot of use cases.

 

[Jovialis]

Awesome, the file finished processing, and now I have 99.99% genotype coverage


Nevertheless, my super kit which was around 97%, almost exactly overlaps over the Nebula file. Still it is good to verify this is the exact position.

Also, Nebula recovered nearly a million more SNPs than I had in the superkit

> Total SNPs Nebula: 2,077,638
> Total SNPs Superkit: 1,224,690

@
Archetype0ne

The medical part is pretty fascinating actually, though for $500, I think it is more worth it to obtain a 30X genome sequence for ancestry research. Especially if you have only tested with one or two companies, and do not have a superkit.

I thought this report was pretty cool!:80: :76:

 

[Archetype0ne]

Awesome, the file finished processing, and now I have 99.99% genotype coverage


Nevertheless, my super kit which was around 97%, almost exactly overlaps over the Nebula file. Still it is good to verify this is the exact position.

Also, Nebula recovered nearly a million more SNPs than I had in the superkit

> Total SNPs Nebula: 2,077,638
> Total SNPs Superkit: 1,224,690

@
Archetype0ne

The medical part is pretty fascinating actually, though for $500, I think it is more worth it to obtain a 30X genome sequence for ancestry research. Especially if you have only tested with one or two companies, and do not have a superkit.

I thought this report was pretty cool!:80: :76:

Thats quite dope!

Could you show me a snip of the health diet section?

 

[Salento]

@Jovialis
If you compare the Nebula coordinates vs 23andme, Ancestry, LivDNA, … Which is the closest and the farthest from Nebula?

 

[Jovialis]