def read_reference(filename):
    """
    Read in WT reference sequence.

    Args:
        filename (str): Name of the file to be read.

    Returns:
        Reference sequence, stripped of trailing newlines.
    """
    with open(filename, 'r') as f:
        ref = f.read()
    ref = ref.splitlines()
    assert len(ref) == 1
    return ref[0]