Next generation sequencing offers a lot of extremely interesting opportunities, but it also presents us with at least as many difficulties – especially when you are working with ancient DNA. I have already touched upon the problem of primer contamination in the data in a previous post. Here, I want to mention a few problems with PCR artifacts.

Next generation sequencing: A somewhat detailed discussion on how to look for and remove primer fragments from your reads when dealing with paired end data. The problem is general although the setting here is ancient DNA sequenced using the Illumina pipeline.