Additional file 1: of Reproducibility of Illumina platform deep sequencing errors allows accurate determination of DNA barcodes in cells

The script ‘barcodecleanup.R’ applies the clean-up procedure as described in the main text. It expects an input file consisting of a table with read counts, organized such that the columns represent the different samples and the rows represent the different barcodes. A detailed explanation of the requirements for the input file is given in the commentary of the script, and an example input file ‘testartificialdata.txt’ containing example artificial data is also provided. Barcodes containing at least one position with an ‘N’ should be removed from the input file and the barcodes should be sorted on the basis of total read count in descending order. Based on user-provided parameters (such as maximal sequence similarity between presumed correct mother-daughter pairs), the algorithm delivers two output files representing barcodes considered correct and those considered incorrect. (R 6 kb)

脚本`barcodecleanup.R`可执行正文中所述的条码清理流程。该脚本要求输入文件为一张读取计数表格，其中列对应不同样本，行对应不同条码（barcode）。输入文件的具体格式要求已在该脚本的注释中详细说明，同时还提供了包含示例人工数据的输入文件`testartificialdata.txt`。需从输入文件中移除所有包含至少一个‘N’的条码，并按照总读取计数从高到低对条码进行排序。根据用户提供的参数（例如推定的正确母-子序列对之间的最大序列相似度），该算法将生成两个输出文件，分别存储被判定为正确与错误的条码。（R 6 KB）