MiSeq Aims for Ion Torrent

     Illumina has released a MiSeq dataset for E.coli MG1655 on its website.  Accompanying the FASTQ and BAM files is a presentation, the first half of which compares the performance to big brother HiSeq.  The second half is an explicit comparison against the available Ion Torrent. 

A first peek at data from an Ion 316 chip

      Ion Torrent has made available an E.coli DH10B fragment dataset for the 316 chip, which is expected to be generally available early next month.  I've theoretically had access to the data since Saturday, but a series of events (computer-free weekend, a crashed home computer, a personal day & a good but unbloggable conference) have meant that ambitious plans to analyze it are still in progress.  So, what I discuss below is either from Ion's provided information or other sources, so take it with appropriate caution.

Two administrative notes

Two administrative items:

First, sometimes comments are getting moderated very late.  I do pledge this is not an attempt on my part to bury negative commentary.  Rather, it appears that sometimes when I thought I had moderated comments via my Android phone it hasn't succeeded.   

Second, I am trying out the new smartphone-friendly layout option for Blogger.  Please let me know if you are reading this on a smartphone and hate the new layout.

E.coli Outbreak Genomics

     The E.coli outbreak in Germany continues to be a major news item.  It is looking increasingly doubtful that the source of the infection will be conclusively traced, as the German authorities have already named and then backed off two suspects, Spanish cucumbers and German bean sprouts.  These activities have not been without repercussions; Spanish agriculture has been hard hit and exports of European produce in general are reportedly hurting.

     On the genomics front, the outbreak has demonstrated how quickly bacterial genomics can be run on the current class of instrumentation.  BGI Europe knocked off the sequence in a series of Ion Torrent runs in 3 days, and a group at University of Muenster worked at similar speed with the Ion setup as well.  Later, sequences have come in from the Illumina and 454 platforms.  The public release of this data has engendered a number of public analysis projects.

The Arsenic Bug, Revisited

As has been covered in many outlets, Science has released eight technical comments on the arsenic-loving bacterium issue along with a response by the authors, which I commented on when it appeared.  A good summary of the comments can be found at In The Pipeline, and Fejes.ca has a good take on it as well.  The quick summary is that various technical and theoretical issues are presented by the critics, and the NASA team dismisses all of them by standing by their data and interpretations.