I would recommend talking to a local genetic counselor. They may be able to find a genomics core that will fit your needs, and they will be able to help you interpret that data in a medically relevant way.
As a heads up, like the commenter on your blog mentioned, you can write to `/dev/rdisk?` to speed up your transfer. You can also view dd's progress by using pv (available in Homebrew) like: `pv /path/to/image.iso | sudo dd of=/dev/rdisk? bs=?M`
That aside, interesting article. All these new ultra-cheap computers are exciting.
I'm not the parent commenter and I'm not on a Mac, but I assume it's the bash glob for a single character match (much like * matches multiple characters, ? matches a single character).
Which means the actual file path should be something like `/dev/rdisk0`.
Edit: oh, I guess you meant the ? in `bs=?M`, in which case I don't know. Probably damurdock's way of not committing to a particular value in their post.
FASTR specifically applies to research being published in peer-reviewed journals and specifically excludes:
>classified research, research resulting in works that generate revenue or royalties for authors (such as books) or patentable discoveries, to the extent necessary to protect a copyright or patent
How was the process of signing up for the PGP? I've been interested in doing it before, but wasn't sure if it would be a major hassle or more of an in-and-out of the doctor thing.
Also I'm impressed at the amount of data, I expected a few VCF files, not a ~60GB BAM.
We're still years off from sequencing at home for anyone other than dedicated biohackers. The MinION is really cool, but it's very much an advanced researcher's tool.
Honestly, if you're interested in having your genome sequenced/analyzed, I would suggest contacting a local genetic counselor and asking if they can find a sequencing core (or someone that does beadchips) that would agree to delete your data after analysis. They would also be able to discuss your data and the impact it has on your health with you, and provide referrals if more testing or diagnosis is needed.
I figured that was probably the case; even optimistically, the Minion costs around $1000. But the parent comment seemed rather too absolute in rejecting sequencing at home, like it'd never happen. I'm going to wait a few years and then reevaluate the choices.
Human Genome patents are no longer recognized in the US[0], but my understanding is that they were used to protect genetic tests and treatments. For example, Myriad Genomics held patents against the BRCA genes (which can indicate breast cancer risk) which they used to prevent competitors from creating BRCA-based panels.
Pathogen identification is indeed a very exciting application for NGS. In case you're interested, here[0] is a paper about a tool called SURPI (Sequence-based Ultra-Rapid Pathogen Identification) which was designed for that purpose. Also, here[1] is a case report from the NEJM where SURPI was used to diagnose a patient with Neuroleptospirosis, which allowed him to be treated quickly and eventually recover. SURPI isn't the only horse in this game, of course, but I've worked with it before so it immediately came to mind.
[0]: "A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples" http://genome.cshlp.org/content/24/7/1180.long
The clinical work they're doing is great, but the code is problematic. Its a bunch of Perl and Python duct taped together with shell scripts.
From the github repo:
My family (rural SE US) uses Wildblue (now Exede) satellite internet. It works better than the dial-up alternative surely, but it falls flat in terms of speed, cost, reliability (you must maintain LOS, so rain, tree growth, and sometimes very thick cloud cover will kill it) and latency (~1000ms ping) compared to my mediocre cable plan. There is also a rolling 30-day bandwidth limit. Another common satellite provider is HughesNet, they have similar plans but do data limits differently IIRC. If satellite is your only choice, it's workable, but do check other options.
Another common rural option is a Wireless ISP (WISP), but they have limited coverage so it will entirely depend on where you are. Also check if DSL is available, it's not the most common thing but it can pop up in strange locations.
