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This script is still under development.

The main script is find_coverage.sh. It requires:
1) Design library CSV file (DesignLibraryDetails_ODD126.csv)
2) a reference genome, including the mtDNA sequence (ref_and_mt.fa)
3) Text file containing the names of the data sets (WITHOUT the file extensions), and data sets of reads (fastq.gz) to be aligned.
4) The sequences of the plasmids used in the experiment (ODD126_augmented_CB39.fasta)
5) The Python script (compare_coverage.py)

The script creates and indexes a graph based on the reference genome and homology arms. Then, for each data set, it aligns the reads to the graph, outputs a .gaf file, and then calculates the coverage of the homology arm and reference genome subpaths (which outputs a .tsv file).

The output is a .tsv file containing hom_arm_name, hom_arm_coverage, ref_subpath_coverage, #_of_hom_arm_edges, count_for_hom_arm, #_of_ref_subpath_edges, and count_for_ref_subpath as columns.