Multiplex Adaptome Capture Sequencing (mAdCap-Seq)

Scripts and data files for the analysis pipeline described in "High-throughput characterization of mutations in genes that drive clonal evolution using multiplex adaptome capture sequencing".

Overview

• reference contains sequence files for the targeted genes of interest and the E. coli REL606 genome with these regions masked out.
• consensus_read_generation has the script for using unique molecular identifiers to perform error correction on raw Illumina reads.
• breseq_postprocessing has the script for converting raw output generated by running breseq on these files into a format with the read counts supporting the reference versus variant alleles.
• trajectory_analysis contains the main scripts for filtering and analyzing the trajectories of mutation frequencies.
• LTEE-compare and protein_structure contain scripts and information for further analyzing the sets of predicted mutations.