Organization of output and metadata files: The metadata parent directory contains subdirectories: common metadata for entire set of experiments (samples_metadata.csv, samples_replicate_numbers.csv, schema_of_files, svg illustration of workflow of experiments) gDNA_Runs processed data from the genomic DNA runs PCR_Stds_Runs processed data from the PCR standards runs script_files python and SGE scripts for processing the data tem_meta_lines temporary folder for collecting metadata for each sample gDNA_Runs and PCR_Stds_Runs subdirectories have same structure and contains subdirectories: ave_error_at_each_pos csv of error at each position for each gDNA sample : one column per sample filtered_reads_tables the table of reads meeting the read length filter with tag sequence, read sequence, and matching qualities group_quals tables of each sample with median qual at each position for each tag group group_size_histos tables of each sample group sizes (read depths per tag) and how many groups with the given read depth lengths_tables tables of each sample of how many reads had the indicated read length nucleotide_counts_tables The number of each nucleotide at each position for each sample, the total groups, error at each position, and nucleotide fractions at each position script files python python files SGE bash and Grid Engine scripts for job submission to hpc temp_meta_lines header.csv The header to which the individual sample metadata is appended header_list The header in a one-line-per column title list (more human readable than the csv version)