j Raw sequence reads

We propose the use of a 405 nm laser to excite the cofactor F420. The study tested this excitation source for precise determination of abundance and autofluorescence intensity of F420 fluorescent cells in a variety of methane producing microbial communities. These include a methanogenic enrichment culture and several communities from continuously operated digesters fed with industrial grade renewable or lab-designed substrates. We present a method including quality control steps for a reliable application in biogas reactor environments. The procedure was verified by MiSeq sequencing of flow cytometrically sorted subcommunities and T-RFLP analysis of whole samples. The cleaned sequence reads of this study without any normalization procedure are available in this BioProject file. If you have any question, please ask to the corresponding author [e-mail].