This disclosure generally relates to improved methods, compositions, and systems for detecting, quantifying, and characterizing genomic sequences from heterogeneous genomic samples. The disclosed methods include providing a unique molecular identifier to the initial target sequences prior to amplification and addition of indexing barcodes. The methods, compositions, and systems can be employed to accurately detect and quantify operational taxonomic units from heterogeneous samples and further to detect sequencing errors, e.g., chimeric sequences, which may occur during the development and sequencing of the library.