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Thread: Dante Labs Long Read Test

  1. #21
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    I received my Long Read kit today, Thursday April 11, I ordered it on Monday, so just three days. The kit appears identical to the 30X short read test from Dante Labs. However, there was no return shipping label enclosed, I just emailed them with a request for that.
    YFull: YF14620 (Dante Labs 2018)

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     MacUalraig (04-11-2019)

  3. #22
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    Looks like Dante Labs raised the price on the long read test, although things are bit confusing, I think they lowered it first so looks like 849 => 799 EUR => 899 EUR to me. If memory serves, processing time went up from 4 to 8 weeks to 8 to 10 weeks. Both change suggest they were surprised by demand... meanwhile, still no reply to my questions about the product.

    Someone said on another thread they received a reply within minutes, has anybody else been able to get any response about the Oxford Nanopore Long Read sequencing? I was eager to get to be among the first to get to play with the results, but if they don't provide actual raw FAST4 data at the same price, I may have to wait until someone does, as well as for the processing time to fall back down. And of course, not responding to queries while raising the price is a good way to lose a customer...

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  5. #23
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    I sent them that query about the discount I omitted to apply and have not received a reply :-(
    Last edited by MacUalraig; 04-11-2019 at 03:24 PM.
    YSEQ:#37; YFull: YF01405 (Y Elite 2013)
    GEDMatch: A828783 (autosomal DNA), 9427684 (GEDCOM) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT
    WGS (Full Genomes Nov 2015, YSEQ Feb 2019, Dante Mar 2019) - further WGS tests pending ;-)
    Ancestry GCs: Scots in central Scotland & Ulster, Ireland; English in Yorkshire & Pennines
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  6. #24
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    I also spot another oddity, the text says 'N50>20,000 bp' but the graphic alongside has the caption 'N50 > 8000'?
    YSEQ:#37; YFull: YF01405 (Y Elite 2013)
    GEDMatch: A828783 (autosomal DNA), 9427684 (GEDCOM) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT
    WGS (Full Genomes Nov 2015, YSEQ Feb 2019, Dante Mar 2019) - further WGS tests pending ;-)
    Ancestry GCs: Scots in central Scotland & Ulster, Ireland; English in Yorkshire & Pennines
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  8. #25
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    Quote Originally Posted by MacUalraig View Post
    I also spot another oddity, the text says 'N50>20,000 bp' but the graphic alongside has the caption 'N50 > 8000'?
    I'm not sure if that's actually how they mean it, because yeah, it would be confusing to everybody. But technically there's no conflict between those claims, because the other says "average N50>20,000bp" and the other "N50>8000".
    Of course, this could technically mean some customers get 8,000bp reads while others get 32,000bp reads which is actually not impossible, but hopefully their quality is more even. (Either way, most of the reads will be possible to join together).

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  10. #26
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    My Long Reads kit arrived, just as I was finishing an early lunch. Now have to wait before I spit.
    YSEQ:#37; YFull: YF01405 (Y Elite 2013)
    GEDMatch: A828783 (autosomal DNA), 9427684 (GEDCOM) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT
    WGS (Full Genomes Nov 2015, YSEQ Feb 2019, Dante Mar 2019) - further WGS tests pending ;-)
    Ancestry GCs: Scots in central Scotland & Ulster, Ireland; English in Yorkshire & Pennines
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  11. #27
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    I should've probably looked at this before asking questions: https://github.com/nanopore-wgs-cons...ome/rel_3_4.md (Not related to Dante Labs, just a sample dataset)
    On a quick count, it looks like the 30X signal-level FAST5 data for Oxford Nanopore weights at about 30 terabytes of data. There's certainly a case for "sneakernet", but at that size it would take a large shipment of hard-drives!
    I do not know if it could be reduced smaller, that page says there's some redundancy and there have been developments on minimizing the files.
    That's bit of a bummer though, because if that's true it practically prevents re-analysis of the signal files at home. The FASTQ & BAM files certainly will be useful. No word if Dante Labs can do the methylation calling themselves. This also having the caveats that the sample preparation must be PCR-free & the methylation profile will be specific to saliva, with whatever degradation has occurred before the analysis. So yea, in summary, I don't know but I wish Dante Labs would tell

    Dante Labs did respond to someone asking on Facebook about the short + long read combination, and their answer was they don't do it now but will look into it. This can be done by third party with the FASTQ/BAM files alone, for example with https://github.com/nanoporetech/ont-assembly-polish

    Also sucks that they raised the price by 100EUR, I want to wait for a better deal now, though to be honest that looks like a very low price, and they should run into legal trouble with their pharmacogenetics report so it's a tough call.

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  13. #28
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    They finally gave me some money back because of having missed the discount code

    You have received a refund

    Total amount refunded: €169.80 EUR

    :-)
    YSEQ:#37; YFull: YF01405 (Y Elite 2013)
    GEDMatch: A828783 (autosomal DNA), 9427684 (GEDCOM) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT
    WGS (Full Genomes Nov 2015, YSEQ Feb 2019, Dante Mar 2019) - further WGS tests pending ;-)
    Ancestry GCs: Scots in central Scotland & Ulster, Ireland; English in Yorkshire & Pennines
    Hidden Content

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     pmokeefe (04-17-2019)

  15. #29
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    Bad news. At first the marketing representative said they would combine both tests (30x short + long reads) to make a complet map without the usual error problems of the Nanopore -wich has a NON random error, unlike PacBio that has more errors but are random-. But after the "technical" consult, they said that they donīt combine tests and donīt know when will they do it (if they do it).
    Methylation is in other question, but we all know the answer "not yet, perhaps in the future, no ETA available". Bad news.

    Wich would be the real advantage of this Test vs a 30x in Fullgenomes/DanteLabs/Yseq??? It appears to be worst than the 10x Chromium of Fullgenomes, but cheaper (less than half).
    Any info about what would this Nanopore test give us? thx

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     pmokeefe (04-17-2019)

  17. #30
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    Quote Originally Posted by Francisco View Post
    Any info about what would this Nanopore test give us? thx
    Short answer: We don't know until we have results and something to compare with.

    Longer answer:
    On it's own I'm skeptical of the value of this test for genetic genealogy. The CNV and SV detection may be useful for medical applications.

    I ordered one of these for the express purpose of hybridizing with a traditional short read 30x WGS test to attempt to get better resolution on the Y chromosome. Mostly the interest is in seeing how many of the STRs in Williams et al (2016), Chromosome-Wide Characterization of Y-STR Mutation Rates, can be resolved but there are also some SNP markers in Poznik's call mask that have failed Sanger validation I'd like to learn more about.

    If I didn't have the 30x WGS test already, I'd be looking at the 10x Chromium instead.

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