As sequencing gets cheaper and cheaper, one would expect the answer for how to best sequence (and assemble!) any given genome would change. Most biologists assume something along these lines: everyone else has achieved some standard coverage (say 10x, or 100x) for their genome, so all we need to do …
read moreThere are comments.
There's been a lot of hooplah in the last year or so about the fact that our ability to generate sequence has scaled faster than Moore's Law over the last few years, and the attendant challenges of scaling analysis capacity; see Figure 1a and 1b, this reddit discussion, and also …
read moreThere are comments.
One of the most important jobs a professor has is to pay it forward: that is, to teach, train, mentor, support, and open up opportunities for their students and postdocs. It's a job that is undervalued by those who focus on the short term -- the administrators and review committees that …
read moreThere are comments.
During our next-gen course, a "student" (really a professor from Australia ;) asked me if I could provide some guidance on what computational infrastructure was necessary to handle next-gen sequencing data. While we used Amazon Web Services during the course, she was interested in finding out if they could use their …
read moreThere are comments.
For anyone who actually wants to know what it is I do, I've updated my lab Web site, http://ged.msu.edu/, to be a bit more representative of what it is we're doing these days. (I wrote it over three years ago, so it's been becoming increasingly dated.) In …
read moreThere are comments.
I just flew back from Montreal, where I gave a talk at the International Tunicate Meeting on the Molgula project. This is a project wherein we are doing quantitative mRNA sequencing on two species of ascidians, or sea squirts -- specifically, on M. oculata (tailed), M. occulta (tailless) -- and their hybrids …
read moreThere are comments.
The second iteration of our bioinformatics summer course, Analyzing Next-Generation Sequencing Data, just finished. It was a great success, at least judging from the comments that people made to us personally; the evaluations aren't yet complete.
The what: a two week course on analyzing next-gen sequencing data, using the Amazon …
read moreThere are comments.