Raspir: A python tool for high-confidence differentiation between rare species of complex microbial communities and background noise. Marie-Madlen Pust and Burkhard Tümmler Clinic for Paediatric Pneumology, Allergology, and Neonatology, Hannover Medical School (MHH), Germany Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Germany Low abundant taxa are assumed to take on strategic roles in microbial communities by introducing tremendous functional flexibility. At the moment, species-level resolution of core and rare species remains challenging due to shared genetic sequences or high sequence similarities between community members or entries in the reference database. We developed a python tool (raspir, rare species identifier), which is based on discrete Fourier transforms and spectral comparisons of biological and reference frequency signals. So, the tool predicts the presence of microbes based on the distribution of short reads mapping towards a circular reference genome. Using the tool, we found that a healthy microbial community structure of the human respiratory tract is associated with higher diversity and absolute abundance of rare species in the early years of life.