Identification of exon junctions includes obtaining a first read sequence based on a detected plurality of signals of a first sequence. A list of exon prefix and suffix sequences are generated by identifying exons of the human genome with a prefix sequence mapping to a suffix sequence of the first read sequence and by identifying exons with a suffix sequence mapping to a prefix sequence of the first read sequence. A pair of exon sequences is selected, with a first exon sequence being one of the exon suffix sequences and a second exon sequence being one of the exon prefix sequences. Summing a number of sequence elements of the first exon sequence that overlap the prefix of the first read sequence, a number of sequence elements of the second exon sequence that overlap the suffix of the first read sequence, and a constant is used to identify a fusion junction.