Pipelines for fitness assay, sequencing, etc. analysis of the VLTE ("very" long term evolution experiment (yeast))

Basic analysis structure: Scripts are run from the directories here. A "Data" directory is kept in the parent directory of this repo, and has these subdirectories: Fitness, Imaging, KV, Other, Ploidy, TSA1_Fluctuation_Assay, WGS (see scripts for full paths to individual data files).

WGS data is at https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP286889 and other data is available as supplementary files of https://www.biorxiv.org/content/10.1101/2020.10.09.330191v1 (you can also look up the title on eLife, where it will be published soon, to find the final version).

Please contact us if you have any questions!