This repository provides a perl script for identifying cross-contamination events that occurred between double-index libraries due to index swapping during library amplification or sequencing:
cross_contamination.plThe script includes a help menu with further instructions and explanations (accessible by executing the script without specifying an input file).
The script has been successfully used with perl 5 (version 30) and has no further dependencies on perl modules or external software.
In what follows we provide an example for how this script was used to determine
cross-contamination using a demultiplexing report file formatted as described
in the help menu of the script. The exemplary input file
(demultiplexing_report_B52992.txt) is provided as part of the documentation.
./cross_contamination.pl demultiplexing_report_B52992.txt >report_file.txtThis script generates text output on the shell (identified cross-contamination events: (i) by event, and (ii) by library), which can be redirected to a file as indicated above.