Rbec is the first ever software specifically developed to precisely characterize the microbial composition from synthetic communities by correcting erroneous bases and identifying the variable amplicon paralogues from the same strain. Rbec can also identify the potential contaminated SynCom samples and derive the contamination sequences for further check. Through the identification of variable paralogues from the same strain, Rbec provides an additional function to normalize the strain abundance by the copy number of amplicon in each strain.