Code used for analysis of viral barcode libraries. Code used for analyzing one-plasmid and ten-plasmid controls is in the controls directory. Code used for analyzing the plasmid, ligated, and viral libraries is in the stock directory. Code used for analyzing barcodes in mouse urine and tissue is in the urine_and_tissue directory. The notebook_combined_stock_bcs.org file is an Emacs Org Mode file that describes the steps used to extract barcodes from the sequencing libraries using cutadapt, cluster the barcodes using Starcode, etc.