1. A method of aligning nucleic acid sequence reads to a reference sequence, the method comprising: (a) receiving a first read comprising the sequence of a first nucleic acid segment from a sample; (b) applying the first read to a Bloom filter to determine whether the first nucleic acid segment is found in a first reference sequence represented by the Bloom filter; (c) receiving a second read comprising the sequence of a second nucleic acid segment from the sample; and (d) applying the second read to the Bloom filter to determine whether the second nucleic acid segment is found in the first reference sequence represented by the Bloom filter.