Hi! Your pseudocode is looking good, and it was straightforward and easy to follow along. I liked how you created a dictionary to store all the lines for each file. One thing I could suggest is checking the code line 29-32. I think an index can contain “N” and therefore not be matched, which should be placed in the junk file, but I think code line 29-32 will put the index that contains “N” into the indexed hopped file (since if the index2 contains N’s, this shouldn’t match index1). One possibility is to specify so that indexes don’t match AND the indexes don’t contain any N’s to be placed into the index hopped file. I hope I understood your code correctly! Other than that, your code looks good! Great job!

Overall, your pseudocode is easy to follow and the logic makes sense! Your high-level functions are useful and relevant to the demultiplexing algorithm.

One idea:
To make your code even more efficient, instead of having multiple code blocks where you check if your quality score is at or above the cutoff, you could wrap lines 18-40 in a single if-else statement to check q-score cutoffs. For example, you could write:

 if quality score < cut-off:
      write to junk
 else:
      your current code from lines 18-40 (not including the q-score checks)

For your pseudocode:

1. Nicely written out and easy to follow.
2. I like how you read all your files at once and store it in a dictionary, clever idea
3. Remember to close your open files at the end

Optional:

1. Include your quality score cutoff as your first conditional statement, b/c if that isn’t met, there's no use of going through your other conditional statements.

Nice work ☉ ‿ ⚆