Dante Labs Kind Of Suck? Maybe?
UPDATE: The following is based on a sample run in September 2022. As someone on the Discord pointed out, Dante appear to have moved to blood samples. This likely improves their results, but I’d still be concerned about the process issues mentioned below.
Over on twitter I’ve been talking about a sample I had run at Dante labs. This was prompted by seeing another of their $200 genome offers appearing in my inbox.
Dante Labs has kind of a checkered history, having had very long processing times and sending out used kits to customers.
For a long time however, they’ve were the only game in town if you wanted a reasonably cheap human genome as a consumer (this is no longer true).
I’m not so interested in their reports personally, but they deliver fastq’s and BAMs too which you can use for your own analysis...
The first genome I ordered from them went fine, nice clean 30x genome. Took some time, but I was able to download the BAM and Fastq’s without issue.
The second sample, not so much. I downloaded the sequence data and began to poke around… but something seemed… off. It didn’t really look like average coverage/depth was anything like 30x. So I looked at the samtools reports and…
Yep… as you can see average depth is about 15x and is dropping below 10x on several chromosomes. The overall read count was fine, but BLASTing unaligned reads showed that they were likely contaminants.
While I’m not interested the reports, I can’t imagine they are valid… so anyway I contacted customer services, providing the output shown above. Here’s what they had to say…
To be clear, I’m not going to go into details but I almost certainly screwed up the collection here. So, I wouldn’t expect a refund. But errr… “the amount of gigabases is enought to provide the results of Sequencing”… no… it is not enought.
They also provided the breakdown below showing that it was 50% contaminated:
So… I probed further… probably I should have said at this point I would be willing to pay to rerun the sample to get sufficient coverage. That’s a screw up on my side. But I get that they would not be able to provide a refund.
I kind of left it at this point, I was considering going through the reports and finding reported regions which are very low coverage (I’m almost certain there would be some). However given this was September last year and I’ve not done this yet, it seems unlikely that I will and I thought it might be of interest to put this out there anyway.
As far as I’m concerned the two major screw ups on Dante’s side are:
They didn’t report I only had 15x not 30x coverage (and provided their standard reports).
Didn’t provide an option to get the full 30x (pay to rerun the library etc.)
After this experience with Dante I moved to Nebula. They use a swab based collection rather than Saliva. This seems more reliable and I’ve not had an issue with them so far, turn around time has also been good. They currently have a sale on for a $175, you need to check the terms though because they’ll automatically subscribe you to yearly reports.
Anyway… I hope that was useful to someone. Consumer grade genomes can be a bit hit-and-miss so be careful. Here’s hoping I don’t get spike-d for this.
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