I'm interested what biological contaminants can effect the net result of sequencing.
I've read some things about it (like this here: http://www.ncbi.nlm.nih.gov/tools/vecscreen/contam/), but have no experience as to when the different sources of contamination are expected. For instance, it states that "DNA/cDNAs from the biological source organism/organelle are usually inserted into a cloning vector".
What does "usually" signify? What is the alternative?
How do the biological contamination sources differ in the different sequencing approaches (genome / transcriptome / exome)?
Is there some online resource where I could get an idea of all the steps involved? I've watched a couple of videos and they are ~5 minute explanations, but vague on the details. I would like a rather comprehensive and detailed guide.