Find_Index_Hopp

Author: Wyatt Eng

Goal: This python3 script is designed to identify index swapped records from the 'Unidentified' output files post demultiplexing.

Required Input

• -U1 : The path to a fastq file containing the undetermined reads from R1.
• -U2 : The path to a fastq file containing the undetermined reads from R2.
• -I : File of known indexes. With each index separated by a new line.

Example Run:

python3 Identify_Index_Swap.py -U1 Undetermined_S0_L008_R1_001.fastq.gz -U2 Undetermined_S0_L008_R2_001.fastq.gz -I seq_indexes.txt