Paste left read and right read from Illumina into a single megaread

mergePairedReads.rb

#!/usr/bin/env ruby

require 'dna' # gem install dna

left, right = ARGV[0], ARGV[1]

left_handle  = File.open(left)
right_handle = File.open(right)

left_records = Dna.new(left_handle)
right_records = Dna.new(right_handle)

left_records.zip(right_records).each do |l, r|
  
end

Are you doing this before or after quality trimming?