Best 454 Applications????

[NGSsequencer]

Hi All,

I am new to the 454 space and am trying to understand what the best applications for the 454 technology are today with competing read lengths are beginning to creep closer to at least the Junior.

Is there an application besides de novo sequencing?
Is exome sequencing viable on a per base cost?

[krobison]

I wrote on this very topic recently: http://omicsomics.blogspot.com/2013/...great-for.html

I'm tending to the feeling that 454 is holding on because of inertial forces; if a study was started on one technology it is viewed as risky to switch. If you need lots of data, use Illumina. If you need long high-quality reads, go with PacBio circular consensus. Just long: go PacBio.

One commenter did point out the truth that 454 reads come out ready-to-go, whereas there are some more complicated informatics involved with some of the proposed alternatives. But these really aren't very hard to manage either; PacBio has good directions on setting up an Amazon cluster to run their protocol, and if you use spot instances (easy to do via STARCluster) the data to get a microbe down to a handful of contigs should be well under US $100.

Jr seems in a particularly dicey position: merged Illumina paired end reads and Ion are both in the same length range, and you get so many more for your money. I'd be really curious to hear someone who exhaustively evaluated the benchtop space & still chose Jr, if such a person can be found.