I think some biologists have a bit of a blind spot for bioinformatics when it comes to critical thinking. There may be a bit of a ‘well, the computer says this, therefore it is true’ attitude.
I think that any biologist who is interacting with bioinformatics/NGS results should take the following steps:
1. Take a complete reference genome from NCBI
2. Turn it into fastqs using e.g. pIRS
3. De novo assemble those fastqs. Oh, look at that, gives you a load of contigs!
4. Compare those contigs against the reference – start sweating.
5. Map your reads back to your contigs.
6. Call variants from that alignment – how does this strain have variants compared to itself? Have I created a new form of life, capable of mutating in silico? No, you haven’t.
7. Go and lie down in a dark room