Fig. 1

Overview of the main functionality of mutscan. A Multiplexed assays of variant effect experiments are based on the enrichment and depletion of protein variants in an assay that selects for a desired activity of the given variants. Enrichment and depletion are quantified using high-throughput sequencing. B The digestFastqs() function processes the FASTQ file(s) for each sample independently and encompasses filtering of low-quality reads and reads with more than the allowed number of mutations, extraction of read components, and aggregation into a vector of counts for variants of interest. C The output objects from digestFastqs() are then combined into a joint SummarizedExperiment object which is in turn provided to downstream functions in mutscan, or one of the many other R packages based on SummarizedExperiment objects, for statistical analysis and plotting. For more details about the individual steps, see the main text