Fig. 1.

Index building. s + 16 bases at every k steps of genome and/or transcriptome reference sequences are indexed, where s and k are user parameters with default values 8 and 4, respectively. Nodes of level (lv) n (n > 0) store positions of sequences of length (s + n) within the reference. For example, the positions of ‘AACTGCTTT’ are stored in the lv1 node (which is a leaf node). The node is a leaf node if the number of stored positions is <32 or the maximum number of levels (16) is reached. See text for details