I think a safe $ estimate for a 20-25x Promethion run is around $700. Of course, theoretically it can do more (sometimes over 30x) but then you start running into issues of flow cell variability and the moment you need to use two flowcells it jumps to $1400.
This is only half the issue with human implementations though. Errors made by the ONT systems are not as well accounted for in the variant calling pipelines, especially compared to Illumina's. This is a general statement with many nuances but the inevitable outcome is the following: You will get pathogenic variants you must validate at much higher rates, and the cost of these variants will send your per patient costs to the moon. Furthermore, the majority of these will come back false positive, as was my experience. In other words, if the variant calling isn't as accurate, this costs from this will be a comparable or even larger pain point. I'd love to see more data on that whole implementation from PacBio.
I think a safe $ estimate for a 20-25x Promethion run is around $700. Of course, theoretically it can do more (sometimes over 30x) but then you start running into issues of flow cell variability and the moment you need to use two flowcells it jumps to $1400.
This is only half the issue with human implementations though. Errors made by the ONT systems are not as well accounted for in the variant calling pipelines, especially compared to Illumina's. This is a general statement with many nuances but the inevitable outcome is the following: You will get pathogenic variants you must validate at much higher rates, and the cost of these variants will send your per patient costs to the moon. Furthermore, the majority of these will come back false positive, as was my experience. In other words, if the variant calling isn't as accurate, this costs from this will be a comparable or even larger pain point. I'd love to see more data on that whole implementation from PacBio.
Yes, I'm largely in agreement with this statement. A 20x PacBio genome seems like a great proposition for the human genetics applications you mention.