Your mission, should you choose to accept it, is to reproduce major findings of a Science paper in just 60 seconds.
This recipe is based on a fun diversion that I show during lectures.
The goal of the recipe is to demonstrate that, when properly documented it is possible to reproduce major scientific findings with relative ease and perhaps under a minute.
This recipe reproduces the main results published in the work:
On a properly set up system, and depending on internet bandwidth, the recipe completes under a minute .
Steps taken in the recipe:
bcftoolsfor all alignment files.
snpEffto summarize the types of variations seen
The main results of the analysis can be found in the files:
All that ... in less than a minute. How is this even possible?
It is not magic, it is standing on the shoulders of giants that created tools like
bcftools, SRA and NCBI!
The recommended way to enjoy this analysis is to have the following video playing while the analysis is running:
We found that the theme song makes even the otherwise bland analysis feel super exciting.
1. Disclaimer: It is the second time when the process will take less than a minute, as the SRA files will be already cached on the system. The first time it will be more sensitive to the current network speed. 😉