Not all scripts were ultimately used. However, here is a discription of some of the more important scripts used. Most or all scripts can be run with no options or with --help for additional information.
Compares all pipelines in a given directory. Looks for the Lyve-SET, kSNP, RealPhy, SNP-Pipeline, and SNVPhyl project directories.
Creates a heatmap image from a 2d distance matrix
Runs a given SNP pipeline in a directory. There must be a "reads" subdirectory where interleaved fastq.gz files are present. The first parameter must be a reference assembly fasta file.
Uncover distances between genomes in allele differences. The input file must be an alleles CSV file from BioNumerics.
Create a scatter plot between two or more pipelines
Compare SNP positions in one pipeline vs another and generate sensitivity and specificity