I looked at a few of the scripts and they all lack commenting so I don't understand what their purpose is. It would be good to have a comment block near the top of each script to make it more interpretable to others. For example, I am looking for the script which infers the haplotype-inherited SNPs of the sample and then creates a personalised mitochondrial genome for the second iteration of alignment. But I can't see any script names which would seem to be relevant. Also, what do the numbers in folder names examples1, examples2, examples4 mean? Similarly, the README.md file could be improved. It consists of a bunch of code blocks and outputs with short headings, but no explanations in sentence form.
I looked at a few of the scripts and they all lack commenting so I don't understand what their purpose is. It would be good to have a comment block near the top of each script to make it more interpretable to others. For example, I am looking for the script which infers the haplotype-inherited SNPs of the sample and then creates a personalised mitochondrial genome for the second iteration of alignment. But I can't see any script names which would seem to be relevant. Also, what do the numbers in folder names examples1, examples2, examples4 mean? Similarly, the README.md file could be improved. It consists of a bunch of code blocks and outputs with short headings, but no explanations in sentence form.