I teach an introductory bioinformatics course. For yesterday's lecture I wanted to demonstrate to students just how much you can get done by properly combining all these awesome tools with the unix command line.
And that got me thinking ... so how much can you get done in a day ... how about an hour? ... then .... well, how about a minute ... a minute you say??? ... yeah right that's just crazy talk, sounds like ... mission impossible. Or is it really?
So I googled the Mission Impossible theme song, I found a version that is about 1 minute long and I came up with a challenge with the following rules:
- You may use any tool or background information that can be reasonably expected to be on a bioinformaticians' computer.
- You have to start with an empty folder
- Start the music and your script. Your script needs to finish before the theme song.
- At the end of the run your folder needs to contain a piece of information that on its own is noteworthy and publication quality information (say an essential part of a prior publication)
All right then - and here is my entry. It produces all major single nucleotide polymorphisms of the 2014 Ebola genome as published in Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak Science 2014. It requires parallel, efetch, bwa, samtools and freebayes.
The script follows. Let me tell you running it while the theme song is on makes it surprisingly exciting!
It even wastes 16 seconds for dramatic flair. Still finishes in time on a MacBook Air while running a presentation.