Improving the Accuracy of Bulk Fitness Assays by Correcting Barcode Processing Biases.

ABSTRACT: Measuring the fitnesses of genetic variants is a fundamental objective in evolutionary biology. A standard approach for measuring microbial fitnesses in bulk involves labeling a library of genetic variants with unique sequence barcodes, competing the labeled strains in batch culture, and using deep sequencing to track changes in the barcode abundances over time. However, idiosyncratic properties of barcodes can induce nonuniform amplification or uneven sequencing coverage that causes some barcodes to be over- or under-represented in samples. This systematic bias can result in erroneous read count trajectories and misestimates of fitness. Here, we develop a computational method, named REBAR (Removing the Effects of Bias through Analysis of Residuals), for inferring the effects of barcode pr

SUBMITTER: McGee RS 

PROVIDER: S-EPMC11316221 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature