Illumina's New Lineup

Illumina made a brace of big hardware announcements at this week's J.P. Morgan conference, and Mick Watson has done a nice job of covering them.  I'll try to cover some different points that have occurred to me after letting the news ferment -- plus Illumina made yet another announcement tonight that scotched a portion of an earlier draft of this piece.

Relearning Chemistry

An evening ritual is to inquire what homework requires assistance, and at the beginning of the year it was a science worksheet as part of an introduction to chemistry.  That, and a later project, have exposed how much rust my knowledge of chemistry has accumulated, but also have led me down the path of repairing forgotten bits and certainly learning some new stuff

Envisioning The Perfect Scaffolder

Rather than make any New Year's resolutions of my own, which I would then feel guilty about not keeping, I've decided to make one for someone else: they will write the perfect open source scaffolder.  There's a lot of scaffolders out there, both stand-alone and integrated into various assemblers, but none are quite right. 

If you are sequencing an isolated bacterium or archean and are looking for a scaffolder, except in a few rare cases, you're doing something wrong: given enough long reads from PacBio it should be possible to solve nearly every bacterial genome. But, if you're sequencing eukaryotic genomes or any metagenome (or you're unlucky or data short on a simple microbial genome), you're probably in the market for one.  I'm going to supply a list of attributes I cooked up during a long drive up the Eastern Seaboard today, without much regard for feasibility or even if some conflict with each other.