Fraunhofer Institute for Toxicology and Experimental MedicineThe amplification of DNA or RNA from low-input samples introduces a substantial amount of noise in next-generation sequencing data. This noise is mainly due to an unequal amplification efficiency of different genomic/transcriptomic regions or sequence errors introduced by the polymerase. These features, which are specific to amplified data, must be thoroughly considered in any downstream bioinformatics analysis. At Fraunhofer ITEM, we either use carefully selected open-source tools that we adapt and integrate into our analysis workflow or we develop our own innovative tools to address specific questions.