An Incomplete Guide to Asking for Help on Your De Novo Genome Project

I've been thinking about this piece for a while, because I am a frequent presence on SEQAnswers.com and often dive into questions regarding de novo sequence assembly, particularly for small genomes.  It's good to help out and a way to feel like one is contributing to a broader community, but sometimes it can be very frustrating because the seekers (SEQers?) of help do not post their questions very well.  So, it would be helpful to have a post to point them to, though I'm sure there are considerations I either haven't thought of or will fail to remember to add.  So, those can either go into the comments or a future post, or perhaps something can go in the Wiki at SEQAnswers.

But in general, think of it this way: you have some experienced hands in a field you wish to enter, who are willing to give detailed advice for free.  But, they can't give that advice unless you specify your question well, and if you don't get it right the first time they may not see (or may ignore) your second shot.

What Might Knock Illumina Off Its Perch?

The big sequencing platform news this week is Roche's announcement that they are ending their collaborations aimed at developing new sequencing technologies.  A collaboration with DNA Electronics aimed to create an Ion Torrent-like system whereas a more ambitious effort with IBM aimed to create instruments based on "DNA transistors".  As noted by Forbes' Matthew Herper in a thought-provoking piece, Illumina is sitting very high atop the sequencer market.

For What is a 454 Still Great?

I've been mulling this item ever since AGBT, but have struggled with the title.  I don't want to sound like I have a grudge against 454 ( truth is I just got some good datasets off this technology), but I do believe that they are few papers away from being stampeded.  Or perhaps not; perhaps the community is really wedded to this platform.

PacBio Back of the Envelope Numbers

Back-of-the-envelope calculations can be quite useful, but also quite dangerous.  They are meant to be quick estimates, but can't be taken too seriously.  Still, I try to get them right & deeply regret overestimating recently on Twitter the cost of a human genome on PacBio by 3X.  Twitter is particularly dangerous: tempting to fire off a note, but impossible to pack in the full calculation

Post AGBT: A Longish Item on Long Sequencing

As others have noted, a significant theme at AGBT this year was sequencing at length.  While this year lacked true bombshells, PacBio impressed many with their making single-contig bacterial genome assemblies look easy.  Moleculo had been the object of much pre-meeting excitement, and while very few additional details emerged about their process, several talks showed what could be done.  As I have discussed previously, Nabsys demonstrated their “positional sequencing” system to select invitees in a hotel suite.  Optical mapping from OpGen and BioNano Genomics featured in a few posters, but did not attract much attention.  Oxford Nanopore had no physical presence, beyond a somewhat secretive suite, but several ONT staffers were happy to reiterate their confidence that they will launch their system – when it is good and ready.

AGBT: Nabsys unveiled

In the previous post I described the Nabsys positional sequencer. Yesterday I got o see it running in their hotel suite here at AGBT13.

AGBT Preview: Nabsys

A complaint which seems to be circulating on Twitter and elsewhere is that this year’s AGBT conference on Marco Island next week doesn’t look like it will have any excitement around new platforms.  AGBT has been a traditional coming out party for platforms.  Last year it was Oxford Nanopore which created a huge buzz, and in previous years that crown has been held by Ion Torrent, Pacific Biosciences, Complete Genomics and others (including a few which seem to have gone kaput).

It is hard to argue that this year’s program is much more heavily tilted towards applications of genomics than novel genomic technologies.  Many of the genomic technology talks are updates on the evolution of existing platforms such as PacBio and Illumina (especially the Moleculo technology).  But, there will also be novel technologies.  

This past fall I had the pleasure of spending half a day with the folks at Nabsys, located a short distance from Boston in Providence RI.  Nabsys’s buildings are in a sea of drab parking lots (not to mention sheriff’s cars; a courthouse is nearby), but on the interior were quite pleasant.  I was largely wearing my “day job” hat that day, but Nabsys will be unveiling their instrument at AGBT and has given me permission to talk about what I saw (and reviewed what I've written to make sure I didn't make some dumb errors, though the content is all mine).  Of course, I will update this after I look some more at AGBT.