My collaborator, Marina LaForgia, and I are gearing up to start processing some plant rhizosphere samples for metagenomic sequencing. We collected more samples than we can afford to process (as is life) and are starting to make the hard decisions about which samples to move forward with. This brought us to the topic of whether or not to include positive and negative controls. I think it is fair to say that positive and negative controls are now the standard for amplicon (e.g. 16S rRNA gene) based microbiome studies. However, I have not seen them used very often for metagenomics. So I turned to Twitter and asked if people are using positive and negative controls for metagenomics and if so – what are they using and how they are dealing with the subsequent data. The resulting Twitter conversation can be found as a Twitter Moment below!
tl;dr – I asked if people are using positive & negative controls when performing metagenomic sequencing on Twitter and it looks like people are!