Counting absolute numbers of molecules using unique molecular identifiers

By Teemu Kivioja, Anna Vähärautio, Kasper Karlsson, Martin Bonke, M. Enge, S. Linnarsson, Jussi Taipale. Nature Methods, 2011

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Transcriptomics technologies (2017, background): “identifiers (UMIs) are short random sequences that are used to individually tag sequence fragments during library preparation so that every tagged fragment is unique [67].”
Splatter: simulation of single-cell RNA sequencing data (2017, methodology): “Three of the 19 datasets used Unique Molecular Identifiers (UMIs) [30] and two used full-length 20 protocols.”
Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences (2018, background): “For example, if one considers unique molecular identiﬁers (UMI) [24] and the counts produced following de-duplication in such an experiment, the information content of a low count can be much higher than in standard RNA-seq experiments without de-duplication, and so ﬁltering rules and prior counts…”
Detection of ultra-rare mutations by next-generation sequencing (2012, methodology): “In addition to their application for high sensitivity detection of rare DNA variants, the degenerate tags in our Duplex Sequencing adapters can also be used for single-molecule counting to precisely determine absolute DNAorRNA copy numbers (25, 29).”