Great job guys! Besides covering the task requirements, you took time to add some extra spice.

I especially enjoy the URL: sausage-dna.science! 😀

For each index it took ~1-2hours, while alignment of the sample data to each reference genome took <30min.

In the attached BWA jupyter notebook, in #data understanding cell you can see the following list comprehension:

weird = [elem for elem in seqs if elem not in seqb]

it lists all the elements in the "small" sample (seqs) which are not present in the "big" sample (seqb).

Thanks! We were in a time scramble at the end. This challenge is very interesting, and we think more time should be dedicated to shaping the final solution.