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The script takes four arguments (separated by spaces):
1) First replicate fastq
2) Second replicate fastq
3) Hamming-distance (we use “4” for this size of barcode)
4) Minimum-reads (we use 5, for 5 million reads per replicate)
The output of the script is a filtered set of fastqs (which grabs only reads with correct barcode structure), two lists of min-reads filtered barcodes, for each first and second replicate files, and one table with the barcodes detected in both replicates and collapsed by hamming distance (whitelist_merged.csv).