At our 2012 course on Analyzing Next-Generation Sequencing Data, we talked quite a bit about future sequencing technologies, as well as about what analyses are reasonably cookbook (and which ones aren't).
Here are my thoughts -- yours welcome!
The basic conclusions about sequencing tech were these:
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Brad Chapman (@chapmanb on twitter) wrote and signed a nice review of my submission to the Bioinformatics Open Source Conference. In his review, he said
My only small suggestion is to include some discussion about your reproducibility work during the talk: the Amazon AMI, documentation and reproducible ipython workflows. This ...read more
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I'm a pretty big advocate of anything open -- open source, open access, and open science, in particular. I always have been. And now that I'm a professor, I've been trying to figure out how to actually practice open science effectively
What is open science? Well, I think ...
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I'm pretty proud of our most recently posted paper, which is on a sequence analysis concept we call digital normalization. I think the paper is pretty kick-ass, but so is the way in which we're approaching replication. This blog post is about the latter.
(Quick note re "replication ...
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I'm putting together a computational pipeline for a paper - a Makefile that runs a ton of stuff and outputs files, combined with an ipython notebook file that takes those output files and turns them into figures for inclusion in a LaTeX file. (Yes, very 2000, except for the ipython ...
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If you're like me, we pretend to care about the science in bioinformatics software. But what we really do is try to find reasons not to outright loathe the software -- because, lud knows, there are usually plenty of reasons to hate it.
In no particular order, here are the ...
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(updated to point to http://arxiv.org/).
Authors: Jason Pell, Arend Hintze, Rosangela Canino-Koning, Adina Howe, James M. Tiedje, C. Titus Brown
Abstract:
The memory requirements for de novo assembly of short-read shotgun sequencing data from complex microbial populations are an increasingly large practical barrier to environmental studies. Here we ...read more
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