Sam Nicholls

My back of the envelope worst case calculation indicates 2.8 million decillion decillion possible valid paths so in retrospect, yes it was a bad idea to try and enumerate these to a terminal.

The Tolls of Bridge Building: Part IV, Mysterious Malformations

   Sam Nicholls    3 Comments    Sanger-QC

Following a short hiatus on the sample un-improvement job which may or may not have been halted by vr-pipe inadvertently knocking over a storage node at the Sanger Institute, our 837 non-33 jobs burst back in to life only to fall at the final hurdle of the first pipeline of the vr-pipe workflow. Despite my […]


   Sam Nicholls


   Sam Nicholls    2 Comments    Personal

On Sunday, I arrived in Leuven, Belgium, to begin my two month research visit at KU Leuven. Yes hello I am a Belgian now — Sam Nicholls (@samstudio8) August 2, 2015 Despite my 2pm ferry from Dover, with an aim to avoid or at least take into account the delays as a result of recent […]

The Tolls of Bridge Building: Part III, Sample (Un)Improvement

   Sam Nicholls    One Comment    Sanger-QC

Previously, on Samposium: I finally had the 870 lanelets required for the sample improvement process. But in this post, I explain how my deep-seated paranoia in the quality of my data just wasn’t enough to prevent what happened next. I submitted my 870 bridged BAMs to vr-pipe, happy to essentially be rid of having to […]

The Tolls of Bridge Building: Part II, Construction

   Sam Nicholls    One Comment    Sanger-QC

Last time on Samposium, I gave a more detailed look at the project I’m working on and an overview of what has been done so far. We have 870 lanelets to pre-process and improve into samples. In this post, I explain how the project has turned into a dangerous construction site. While trying to anticipate […]