Methods for standardized sequencing of nucleic acids and uses thereof are described. A method for controlling for non-systematic error in an amplification-based next generation sequencing (NGS) library preparation, comprises: including of an internal amplification control (IAC) sharing identical priming sites to a native nucleic acid target template of interest in a NGS library preparation; mimicing the kinetics of the native nucleic acid target in the amplification reaction, and controlling for sample-, platform-, experiment-, operator- and/or target-specific variation in amplification efficiency.