In this problem set, you’re given DNA sequencing data that, when analyzed by mapping reads and calling variants, reveals a secret DNA message. Here’s a decoder based on Church et al. that decodes DNA sequences stored in the file secret:

For example, try:

• echo "ATGAGACTCTGGACTTCGTCGGGAAATAAGGTATGTATAA" > secret
• echo "CTGGCTCCCTTCGAAAAGGATCATAGTTAAGT" > secret
• echo "CTGAATTCCGGTCGCTCGGCTGTCACTGGTTG" > secret