Couple of small typos/wording suggestions here. I suggest replacing with the following:

This script takes forward and reverse Illumina reads and joins them using the method chosen. Will optionally create an updated index reads file containing index reads for the surviving joined paired end reads. If the option to write an updated index file is chosen, be sure that the order of the index reads is the same as the order of reads in the files that will be joined (this is the default for reads generated on the Illumina instruments).