mtb_ExpEvo

Scripts for data analyzing sequence data from experimental evolution associated with the following publication: eLife2022;11:e78454 (DOI: https://doi.org/10.7554/eLife.78454)

popoolationStats.py

This script takes in alignment files (BAMs) from pool-seq, subsamples to minimize effects of differential coverage and calculates genome wide population statistics (pi and Tajima's D) using Popoolation.

popoolationSyncToTSV.py

Converts Popoolation2 sync file to TSV with allele frequencies. Filters mutations based on bed file, allele count, coverage and frequency across samples.

slidingWindowCoverage.py

This script calculates coverage in sliding windows from BAM(s) and outputs compiled information.