Sunday, 13 March 2011

RNA-seq of a 12GB dataset in less than 7 hours

Folks at CLCbio have updated the CLC Genomics Machine benchmarks with newer datasets and the new hardware configuration. There are two RNA-Seq data sets and a full genome mapping data set, and more will come. All the benchmarks are now using the CLC Genomics Server rather than the Assembly Cell.


  1. Hows the sensitivity and specificity of the mapping? I can map faster by giving random locations :)

  2. Hmmm what do you mean by mapping faster by giving random locations?
    This is not a plug for CLCbio btw, :) I am curious about commercial products and their benchmarking.
    Thus far, I do find CLCbio being rather open in the sense that by publishing benchmarks you are
    1)very sure that your product is the best out there.
    2)inviting others to benchmark and prove that you are not the best.

    which seems fair enough

  3. I didn't do RNA seq (yet), but mapping 23 million sequences to human genome (Gg18) took about 2 hours on a single machine with dual 6-core 2.66 gHz xeons and 48GB RAM

  4. RNA seq is slower when u have to consider spliced transcripts ;)


Datanami, Woe be me