Author Archives: Rob
Introducing pufferfish An efficient index for the colored, compacted, de Bruijn graph
Note: This post describes some cool data structure work (link to the work-in-progress GitHub repo here) my students @fataltes, @hrksrkr, and I have been doing (pre-print coming soon!). If you find these ideas interesting, or you have any interesting thoughts … Continue reading
The RNA-seq abundance zoo
I’m kicking off this year with a rather different kind of post. Actually, I started writing this post some time ago (November 19, 2013!), if the draft log of WordPress is to be believed. I’d been working for some time on … Continue reading
RapMap: Unreasonably Fast and Accurate Transcriptome Mapping
Introducing RapMap I’ve recently been working with my student Avi Srivastava on a new project, RapMap. RapMap is a tool for mapping (see below for the distinction between mapping and alignment) sequencing reads to a transcriptome. It currently implements two related but distinct … Continue reading
Not-quite alignments: Salmon, Kallisto and Efficient Quantification of RNA-Seq data
This past week was the 28th annual Biology of Genomes (BoG) meeting at Cold Spring Harbor. While I wasn’t able to attend the full meeting, I was able to attend on Wed. (the ability to be local and have access to the … Continue reading
What Computer Science Isn’t.
Disclaimer: I want to be clear about my intent in this post. I am absolutely not arguing that programming, software engineering, testing, quantitation and other practical tasks or related fields are not every bit as important as Computer Science. These … Continue reading