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Thread: Nebula Genomics (30x Whole Genome Sequencing)

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    Advisor Jovialis's Avatar
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    Nebula Genomics (30x Whole Genome Sequencing)

    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.

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    Quote Originally Posted by Jovialis View Post
    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.

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    Advisor Jovialis's Avatar
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    ^^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.

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    Regular Member Salento's Avatar
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    Quote Originally Posted by Jovialis View Post
    ^^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 :)

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    Advisor Jovialis's Avatar
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    Quote Originally Posted by Salento View Post
    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.

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    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.

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    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.

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    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.
    Fathers mtdna ...... T2b17
    Grandfather mtdna ... T1a1e
    Sons mtdna ...... K1a4p
    Mothers line ..... R1b-S8172
    Grandmother paternal side ... I1-CTS6397
    Wife paternal line ..... R1a-Z282

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    Quote Originally Posted by Jovialis View Post
    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.

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    Quote Originally Posted by Jovialis View Post
    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.
    There are now almost 6 weeks. Did they notify you if the sample passed the quality control? If not ask them.

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    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.

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    After returning the kit they had not sent me any information, I asked them after a month and a half what the situation of the test was, they told me that it arrived and went into quality control and they would let me know if it passed. After another two months without any notification from them, I asked them again to communicate the status of the test. They gave me the same answer!... Now more than 25 weeks have passed and I only receive apologies and postponement over postponements, for a week or maximum two weeks! And it's very serious because now they don't seem to know about kits or anything...! Now, I have to take steps to return the money and the sample.

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    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?

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    Advisor Jovialis's Avatar
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    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.

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    Quote Originally Posted by Jovialis View Post
    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.
    Any news after 2 and a half months since they told you that the sample entered QC? Like many others, I haven't received any results yet, although they tell me that it has been sequenced for 7 months... and they had promised the result 6 months ago!

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    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.

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    Advisor Jovialis's Avatar
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    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.
    Last edited by Jovialis; 14-08-21 at 03:31.

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    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.

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    Hey Jov. Does this company offer health and nutrition services?
    I bet with such deep coverage this must have a lot of use cases.
    “Man cannot live without a permanent trust in something indestructible in himself, and at the same time that indestructible something as well as his trust in it may remain permanently concealed from him.”

    Franz Kafka

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    Advisor Jovialis's Avatar
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    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!


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    Quote Originally Posted by Jovialis View Post
    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!

    Thats quite dope!

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

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

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    Quote Originally Posted by Salento View Post
    @Jovialis
    If you compare the Nebula coordinates vs 23andme, Ancestry, LivDNA, … Which is the closest and the farthest from Nebula?
    Ancestry gives you the most coverage out of those, 23andme, and LivingDNA are tied for the least. The bulk of the Superkit came from what Ancestry provided.

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    My Y-haplogroup according to what WGSextract found by analyzing the WGS BAM:

    R1b1a1b2a2a

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